From f02d68bd2942dad9de26bacdf5acb8f8c491564b Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 29 Jan 2025 19:39:12 +0200 Subject: [PATCH 01/30] [EDU-474] Data Studios doc audit Fixes https://seqera.atlassian.net/browse/EDU-474 Signed-off-by: Justine Geffen --- platform_versioned_docs/version-24.2/data_studios/index.mdx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/platform_versioned_docs/version-24.2/data_studios/index.mdx b/platform_versioned_docs/version-24.2/data_studios/index.mdx index 17545b580..b157a3c89 100644 --- a/platform_versioned_docs/version-24.2/data_studios/index.mdx +++ b/platform_versioned_docs/version-24.2/data_studios/index.mdx @@ -1,16 +1,16 @@ --- title: "Overview" -description: "Data Studios public preview." +description: "Studios public preview." date: "1 Oct 2024" tags: [data, studios] --- -Data Studios is a unified platform where you can host a combination of container images and compute environments for interactive analysis using your preferred tools, like JupyterLab and RStudio Notebooks, Visual Studio Code IDEs, or Xpra remote desktops. Each Data Studio session is an individual interactive environment that encapsulates the live environment for dynamic data analysis. +Studios is a unified platform where you can host a combination of container images and compute environments for interactive analysis using your preferred tools, like JupyterLab and RStudio Notebooks, Visual Studio Code IDEs, or Xpra remote desktops. Each Studio is an individual interactive environment that encapsulates the live environment for dynamic data analysis. On Seqera Cloud, the free tier permits only one running session at a time. To run simultaneous sessions, [contact Seqera][contact] for a Seqera Cloud Pro license. :::note -Data Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Data Studios in Enterprise is not enabled by default. You can enable Data Studios in the [environment variables configuration](../enterprise/data-studios.mdx). +Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Studios in Enterprise is not enabled by default. You can enable it in the [environment variables configuration](../enterprise/data-studios.mdx). ::: ## Requirements From 9e9aff55d13c97aae7b2659e3b076269df3ea14f Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Mon, 10 Feb 2025 17:24:58 +0200 Subject: [PATCH 02/30] Audit --- .../{data_studios => studios}/custom-envs.mdx | 16 +- .../version-24.2/studios/index.mdx | 163 ++++++++++++++++++ .../version-24.2/studios/managing.mdx | 152 ++++++++++++++++ 3 files changed, 322 insertions(+), 9 deletions(-) rename platform_versioned_docs/version-24.2/{data_studios => studios}/custom-envs.mdx (86%) create mode 100644 platform_versioned_docs/version-24.2/studios/index.mdx create mode 100644 platform_versioned_docs/version-24.2/studios/managing.mdx diff --git a/platform_versioned_docs/version-24.2/data_studios/custom-envs.mdx b/platform_versioned_docs/version-24.2/studios/custom-envs.mdx similarity index 86% rename from platform_versioned_docs/version-24.2/data_studios/custom-envs.mdx rename to platform_versioned_docs/version-24.2/studios/custom-envs.mdx index 41d0e2ab9..8fad711df 100644 --- a/platform_versioned_docs/version-24.2/data_studios/custom-envs.mdx +++ b/platform_versioned_docs/version-24.2/studios/custom-envs.mdx @@ -7,7 +7,7 @@ tags: [data, studios] In addition to the Seqera-provided container template images, you can provide your own custom container environments by augmenting the Seqera-provided images with a list of Conda packages or by providing your own base container template image. -Data Studios uses the [Wave][wave-home] service to build custom container template images. +Studios use the [Wave][wave-home] service to build custom container template images. ## Conda packages @@ -21,7 +21,7 @@ Data Studios uses the [Wave][wave-home] service to build custom container templa ### Conda package syntax {#conda-package-syntax} -When adding a new data studio session, you can customize its configuration to install a list of Conda packages to the template image. The supported schema is identical to that used by the Conda `environment.yml` file. For more information on the Conda environment file, see [Creating an environment file manually][env-manually]. +When adding a new Studio, you can customize its configuration to install a list of Conda packages to the template image. The supported schema is identical to that used by the Conda `environment.yml` file. For more information on the Conda environment file, see [Creating an environment file manually][env-manually]. ```yaml title="Example environment.yml file" channels: @@ -45,14 +45,12 @@ Public container registries are supported by default. Amazon Elastic Container R ### Prerequisites -- Access to a container image repository, either a public container registry or a private Amazon ECR repository -- A container template image +- Access to a container image repository, either a public container registry or a private Amazon ECR repository. +- A container template image. ### Dockerfile configuration {#dockerfile} -For your custom template container image, you must use a Seqera-provided base image and include several additional build steps for compatibility with Data Studios. - -To create a data studio with a custom template image, see [Add a data studio][add-ds]. +For your custom template container image, you must use a Seqera-provided base image and include several additional build steps for compatibility with Studios. To create a Studio with a custom template image, see [Add a Studio][add-ds]. #### Ports @@ -109,14 +107,14 @@ If the custom container template image build fails, the data studio session has To inspect the status of an ongoing build, or a successful or failed build, complete the following steps: -1. Select the **Data Studios** tab in Seqera Platform. +1. Select the **Studios** tab in Seqera Platform. 1. From the list of data studio sessions, select the name of the session with **building** or **build-failed** status that you want to inspect, and then select **View**. 1. In the **Details** tab, scroll to **Build reports** and select **Summary** to open the Wave service container build report for your build. 1. Optional: If the build failed, select the **Error report** tab to view the errors associated with the build failure. -[add-ds]: ./managing.mdx#add-a-data-studio +[add-s]: ./managing.mdx#add-a-studio [wave]: ../enterprise/configuration/wave.mdx [wave-home]: https://seqera.io/wave/ diff --git a/platform_versioned_docs/version-24.2/studios/index.mdx b/platform_versioned_docs/version-24.2/studios/index.mdx new file mode 100644 index 000000000..cc548ad04 --- /dev/null +++ b/platform_versioned_docs/version-24.2/studios/index.mdx @@ -0,0 +1,163 @@ +--- +title: "Overview" +description: "Studios public preview." +date: "1 Oct 2024" +tags: [data, studios] +--- + +Studios is a unified platform where you can host a combination of container images and compute environments for interactive analysis using your preferred tools, like JupyterLab and RStudio Notebooks, Visual Studio Code IDEs, or Xpra remote desktops. Each Studio is an individual interactive environment that encapsulates the live environment for dynamic data analysis. + +On Seqera Cloud, the free tier permits only one running session at a time. To run simultaneous sessions, [contact Seqera][contact] for a Seqera Cloud Pro license. + +:::note +Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Studios in Enterprise is not enabled by default. You can enable it in the [environment variables configuration](../enterprise/studios.mdx). +::: + +## Requirements + +Before you get started, you need the following: + +- Valid credentials to access your cloud storage data resources. +- At minimum the **Maintain** role set of permissions. +- A compute environment with sufficient resources. This is highly dependent on the volume of data you wish to process, but we recommended at least 2 CPUs allocated with 8192 MB of memory. See [AWS Batch](../compute-envs/aws-batch.mdx) for more information about compute environment configuration. +- [Data Explorer](../data/data-explorer.mdx) is enabled. + +:::note +Currently, Studios only supports AWS Batch compute environments that **do not** have Fargate enabled. +::: + +## Limitations + +If you configured your AWS Batch compute environment to include an EFS file system with **EFS file system > EFS mount path**, the mount path must be explicitly specified. The mount path cannot be the same as your compute environment work directory. If the EFS file system is mounted as your compute environment work directory, snapshots cannot be saved and sessions fail. To mount an EFS volume in a studio session (for example, if your organization has a custom, managed, and standardized software stack in an EFS volume), add the EFS volume to the compute environment (system ID and mount path). The volume will be available at the specified mount path in the session. + +For more information on AWS Batch configuration, see [AWS Batch][aws-batch]. + +## Container image templates + +Studios provides four container image templates: JupyterLab, RStudio Server, Visual Studio Code, and Xpra. The image templates install a very limited number of packages when the session container is built. You can install additional packages as needed during a session. + +The image template tag includes the version of the analysis application, an optional incompatibility flag, and the Seqera Connect version. Connect is the proprietary Seqera web server client that manages communication with the container. The tag string looks like this: + +```ignore title="Image template tag" +-[u]- +``` + +- ``: Third-party analysis application that follows its own semantic versioning `..`, such as `4.2.5` for JupyterLab. +- ``: Optional analysis application update version, such as `u1`, for instances where a backwards incompatible change is introduced. +- ``: Seqera Connect client version, such as `0.7` or `0.7.0`. + +Additionally, the Seqera Connect client version string has the format: + +```ignore title="Seqera version tag subset" +.. +``` + +- ``: Signifies major version changes in the underlying Seqera Connect client. +- ``: Signifies breaking changes in the underlying Seqera Connect client. +- ``: Signifies patch (non-breaking) changes in the underlying Seqera Connect client. + +When pushed to the container registry, an image template is tagged with the following tags: + +- `-.`, such as `4.2.3-0.7`. When adding a new data studio container template image this is the tag displayed in Seqera Platform. +- `-..`, such as `4.2.3-0.7.1`. + +To view the latest versions of the images, see [public.cr.seqera.io](https://public.cr.seqera.io/). You can also augment the Seqera-provided image templates or use your own custom container image templates. This approach is recommended for managing reproducible analysis environments. For more information, see [Custom environments][custom-envs]. + +**JupyterLab 4.2.5** + +The default user is the `root` account. The following [conda-forge](https://conda-forge.org/) packages are available by default: + +- `python=3.13.0` +- `pip=24.2` +- `jedi-language-server=0.41.4` +- `jupyterlab=4.2.5` +- `jupyter-collaboration=1.2.0` +- `jupyterlab-git=0.50.1` +- `jupytext=1.16.4` +- `jupyter-dash=0.4.2` +- `ipywidgets=7.8.4` +- `pandas[all]=2.2.3` +- `scikit-learn=1.5.2` +- `statsmodels=0.14.4` +- `itables=2.2.2` +- `seaborn[stats]=0.13.2` +- `altair=5.4.1` +- `plotly=5.24.1` +- `r-ggplot2=3.5.1` +- `nb_black=1.0.7` +- `qgrid=1.3.1` + +To install additional Python packages during a running session, execute `!pip install ` commands in your notebook environment. Additional system-level packages can be installed in a terminal window using `apt install `. + +To see the list of all JupyterLab image templates available, see [public.cr.seqera.io/repo/platform/data-studio-jupyter](https://public.cr.seqera.io/repo/platform/data-studio-jupyter). + +**RStudio Server 4.4.1** + +The default user is the `root` account. To install R packages during a running session, execute `install.packages("")` commands in your notebook environment. Additional system-level packages can be installed in a terminal window using `apt install `. + +To see the list of all RStudio Server image templates available, see [public.cr.seqera.io/repo/platform/data-studio-rstudio](https://public.cr.seqera.io/repo/platform/data-studio-rstudio). + +**Visual Studio Code 1.93.1** + +[Visual Studio Code][vsc] is an integrated development environment (IDE) that supports many programming languages. The default user is the `root` account. To install extensions during a running session, select **Extensions**. Additional system-level packages can be installed in a terminal window using `apt install `. + +To see the list of all Visual Studio Code image templates available, see [public.cr.seqera.io/platform/data-studio-vscode](https://public.cr.seqera.io/repo/platform/data-studio-vscode). + +**Xpra 6.2.0** + +[Xpra](https://github.com/Xpra-org/xpra), known as _screen for X_, allows you to run X11 programs by giving you remote access to individual graphical applications. The container template image also installs NVIDIA Linux x64 (AMD64/EM64T) drivers for Ubuntu 22.04 for running GPU-enabled applications. To use these GPU drivers, your compute environment must specify GPU instance families. + +The default user is the `root` account. The image is based on `ubuntu:jammy`. Additional system-level packages can be installed during a running session in a terminal window using `apt install `. + +To see the list of all Xpra image templates available, see [public.cr.seqera.io/repo/platform/data-studio-xpra](https://public.cr.seqera.io/repo/platform/data-studio-xpra). + +## Session statuses + +Data studios have the following possible statuses: + +- **building**: When a custom environment is building the template image for a new Studio. The [Wave] service performs the build action. For more information on this status, see [Inspect custom container template build status][build-status]. +- **build-failed**: When a custom environment build has failed. This is a non-recoverable error. Logs are provided to assist with troubleshooting. For more information on this status, see [Inspect custom container template build status][build-status]. +- **starting**: The data studio is initializing. +- **running**: When a data studio session is **running**, you can connect to it, copy the data studio URL, or stop it. In addition, the session can continue to process requests/run computations in the absence of an ongoing connection. +- **stopping**: The recently-running session is in the process of being stopped. +- **stopped**: When a session is stopped, the associated compute resources are deallocated. You can start or delete the data studio when it's in this state. +- **errored**: This state most often indicates that there has been an error starting the data studio session but it is in a **stopped** state. There might be errors reported by the session itself but these will be overwritten with a **running** status if the data studio session is still running. + + :::tip + If you encounter an error with the public preview release of Data Studios, [contact Seqera support][contact]. + ::: + +## Session checkpoints + +When you start a session, it automatically creates a *checkpoint*. A checkpoint saves changes that you make to the root filesystem and stores it in the compute environment's pipeline work directory in the `.studios/checkpoints` folder with a unique name. The checkpoint is updated every five minutes. + +When you stop and start a data studio session, or start a new data studio session from a previously created checkpoint, changes such as installed software packages and configuration files are restored and made available in the data studio session. Changes made to mounted data are not included in a checkpoint. + +Checkpoints can be renamed and the name has to be unique per data studio. Spaces in checkpoint names are converted to underscores automatically. + +Checkpoint files in the compute environment work directory may be shared by multiple data studios. Each checkpoint file is cleaned up asynchronously after the last data studio referencing the checkpoint is deleted. + +:::note +The cleanup process is a best effort and not guaranteed. Seqera attempts to remove the checkpoint, but it can fail if, for example, the compute environment credentials used do not have sufficient permissions to delete objects from storage buckets. +::: + +## Session volume automatic resizing + +By default, a session allocates an initial 2 GB of storage. Available disk space is continually monitored and if the available space drops below a 1 GB threshold, the file system is dynamically-resized to include an additional 2 GB of available disk space. + +This approach ensures that a session doesn't initially include unnecessary free disk space, while providing the flexibility to accommodate installation of large software packages required for data analysis. + +The maximum storage allocation for a session is limited by the compute environment disk boot size. By default, this is 30 GB. This limit is shared by all sessions running in the same compute environment. + +If the maximum allocation size is reached, it is possible to reclaim storage space using a snapshot. + +Stop the active session to trigger a snapshot from the active volume. Data Studios uploads the snapshot to cloud storage with Fusion. When you start from the newly saved snapshot, all previous data is loaded and the newly-started session will have 2 GB of available space. + + +[contact]: https://support.seqera.io/ +[vsc]: https://code.visualstudio.com/ +[Wave]: https://seqera.io/wave/ + +[aws-batch]: ../compute-envs/aws-batch.mdx +[custom-envs]: ./custom-envs.mdx +[build-status]: ./custom-envs.mdx#build-status diff --git a/platform_versioned_docs/version-24.2/studios/managing.mdx b/platform_versioned_docs/version-24.2/studios/managing.mdx new file mode 100644 index 000000000..8b7859d0a --- /dev/null +++ b/platform_versioned_docs/version-24.2/studios/managing.mdx @@ -0,0 +1,152 @@ +--- +title: "Manage data studio sessions" +description: "Manage data studio sessions." +date: "1 Oct 2024" +tags: [data, studios] +--- + +Select the **Data Studios** tab in Platform to view all data studio sessions. The list includes the name, cloud provider, analysis template, region, author, creation date, and status of each session. In this view, you can add a new data studio and start, stop, or connect to an existing session. Dynamically filter the list of data studios using the search bar to search by name (default), author username, or compute environment name. Select the data studio to open a detailed view that displays configuration information. + +## Add a data studio + +This functionality is available to users with the **Maintain** role and above. + +To add a new data studio, complete the following steps: + +1. In a workspace, select **Data Studios**, and then select **Add data studio**. +1. For the **Compute & Data** section, complete the following steps: + + 1. Customize the following fields: + - **Select compute environment**: Only AWS Batch is supported. + - **CPUs allocated**: The default allocation is 2 CPUs. + - **GPUs allocated**: Available only if the selected compute environment has GPU support enabled. For more information about GPUs on AWS, see [Amazon ECS task definitions for GPU workloads][aws-gpu]. The default allocation is 0 GPUs. + - **Maximum memory allocated**: The default allocation is 8192 MiB of memory. + 1. Select **Mount data**, and then from the **Mount data** modal, select data to mount. Select **Mount data** to confirm your selection. + + :::tip + Datasets are mounted using the [Fusion file system](https://docs.seqera.io/fusion) and are available at `/workspace/data/`. Mounted data doesn't need to match the compute environment or region of the cloud provider of the data studio. However, this might cause increased costs or errors. + ::: + + 1. Select **Next**. + +1. For the **General config** section, complete the following steps: + + - To use one of the Seqera-provided container templates, complete the following steps: + + 1. Customize the following fields: + - **Container template**: Select a data studio template from the dropdown list. + - **Data studio name** + - Optional: **Description** + 1. Optional: Select **Install Conda packages** to enter or upload a list of Conda packages to include with the data studio. For more information on the syntax for specifying Conda packages, see [Conda package syntax][conda-syntax]. + 1. Select **Next**. + + - To use a custom container template image that you supply, complete the following steps: + + 1. Customize the following fields: + - **Container template**: Select **Prebuilt container image** from the list. For information about providing your own template, see [Custom container template image][custom-image]. + + :::tip + If you select the **Prebuilt container image** template, you cannot select **Install Conda packages** as these options are mutually exclusive. + ::: + + - **Data studio name** + - Optional: **Description** + 1. Select **Next**. + +1. For the **Summary** section, complete the following steps: + 1. Ensure that the specified configuration is correct. + 1. Save your configuration: + - If you want to save the data studio for future use, select **Add only**. + - If you want to save and immediately start the data studio, select **Add and start**. + +You'll be returned to the Data Studios landing page that displays the list of data studio sessions in your workspace. You can inspect the configuration details of the session that you created by selecting the session name. The data studio that you created will be listed with a status of either **stopped** or **starting**, depending on whether you elected to only add the data studio or to start a session as well. + +:::note +By default, data studio sessions only have read permissions to mounted data paths. Write permissions can be added for specific cloud storage buckets during the compute environment configuration by defining additional **Allowed S3 Buckets**. This means that data can be written from the session back to the cloud storage path(s) mounted. To stop potential data loss, only one session per workspace can mount a unique data path. When adding a new session, data paths already mounted to other running sessions are unavailable. If a new file is uploaded to the cloud storage bucket path while a session is running, the file may not be available to the session immediately. +::: + +## Start a data studio session + +This functionality is available to users with the **Maintain** role and above. + +A data studio needs to be started before you can connect to it. From the list in your workspace, select the three dots next to the status message for the data studio you want to start, then select **Start**. You can optionally change the configuration of the data studio, then select **Start in new tab**. A new browser tab will open that displays the startup state of the data studio session. Once the session is running, you can connect to it. A session will run until it is stopped manually or it encounters a technical issue. + +:::note +A data studio session consumes resources until it's **stopped**. +::: + +Once a session is in a **running** state, you can connect to it, obtain the public link to the session to share with collaborators inside your workspace, and stop it. + +## Start an existing data studio as a new session + +This functionality is available to users with the **Maintain** role and above. + +You can use any existing data studio as the foundation for adding a new data studio. This functionality creates a clone of the data studio, including its checkpoint history, preserving any modifications made to the original data studio. When you create a session in this way, future changes are isolated from the original session. + +When adding a new session from an existing session or checkpoint, the following fields cannot be changed: + +- **Data Studio Template** +- **Original data studio session and checkpoint** +- **Compute environment** +- **Installed Conda packages** + +To add a new session from an existing **stopped** session, complete the steps described in [Add a data studio](#add-a-data-studio). + +Additionally, you can add a new session from any existing data studio checkpoint except the currently running checkpoint. From the data studio detail page, select the **Checkpoints** tab and in the **Actions** column, select **Start as new data studio**. This is useful for interactive analysis experimentation without impacting the state of the original data studio. + +## Connect to a data studio + +This functionality is available to all user roles excluding the **View** role. + +To connect to a running session, select the three dots next to the status message and choose **Connect**. A new browser tab will open containing the data studio session. + +:::warning +An active connection to a session will not prevent administrative actions that might disrupt that connection. For example, a session can be stopped by another workspace user while you are active in the session, the underlying credentials can be changed, or the compute environment can be deleted. These are independent actions and the user in the session won't be alerted to any changes - the only alert will be a server connection error in the active session browser tab. +::: + +Once connected, the data studio session will display the status of **running** in the list, and any connected user's avatar will be displayed under the status in both the list of data studios and in each data studio session detail page. + +## Collaborate in a data studio + +This functionality is available to all user roles excluding the **View** role. + +To share a link to a running session with collaborators inside your workspace, select the three dots next to the status message for the session you want to share, then select **Copy data studio URL**. Using this link, other authenticated users can access the session directly. + +![](../data/_images/data_studios_collaboration.png) + +:::note +Collaborators need valid workspace permissions to connect to the running data studio. +::: + +## Stop a data studio + +This functionality is available to users with the **Maintain** role and above. + +To stop a running session, select the three dots next to the status message and then select **Stop**. The status will change from **running** to **stopped**. When a session is stopped, the compute resources it's using are deallocated. You can stop a session at any time, except when it is **starting**. + +Stopping a running session creates a new checkpoint. + +## Restart a stopped data studio + +This functionality is available to users with the **Maintain** role and above. + +When you restart a stopped session, the session uses the most recent checkpoint. + +## Start a new session from a checkpoint + +This functionality is available to users with the **Maintain** role and above. + +You can start a new session from an existing stopped session. This will inherit the history of the parent checkpoint state. From the list of **stopped** data studios in your workspace, select the three dots next to the status message for the data studio and select **Start as new**. Alternatively, select the **Checkpoints** tab on the data studio detail page, select the three dots in the **Actions** column, and then select **Start as new** to start a new session. + +## Delete a data studio session + +This functionality is available to users with the **Maintain** role and above. + +You can only delete a data studio when it's **stopped**. Select the three dots next to the status message and then select **Delete**. The data studio is deleted immediately and can't be recovered. + + + +[aws-gpu]: https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-gpu.html + +[conda-syntax]: ./custom-envs.mdx#conda-package-syntax +[custom-image]: ./custom-envs.mdx#custom-containers From 7b771af67074c55af55f1d7b8b3d3ecbaee4fa9a Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Mon, 17 Feb 2025 23:44:59 +0200 Subject: [PATCH 03/30] Data Studios > Studios plus redirects --- .../{data_studios => studios}/custom-envs.mdx | 6 +- .../{data_studios => studios}/index.mdx | 26 ++++---- .../{data_studios => studios}/managing.mdx | 62 +++++++++---------- .../version-24.3-sidebars.json | 8 +-- static/_redirects | 5 ++ 5 files changed, 56 insertions(+), 51 deletions(-) rename platform_versioned_docs/version-24.3/{data_studios => studios}/custom-envs.mdx (91%) rename platform_versioned_docs/version-24.3/{data_studios => studios}/index.mdx (81%) rename platform_versioned_docs/version-24.3/{data_studios => studios}/managing.mdx (58%) diff --git a/platform_versioned_docs/version-24.3/data_studios/custom-envs.mdx b/platform_versioned_docs/version-24.3/studios/custom-envs.mdx similarity index 91% rename from platform_versioned_docs/version-24.3/data_studios/custom-envs.mdx rename to platform_versioned_docs/version-24.3/studios/custom-envs.mdx index 8df3d8b44..90b336431 100644 --- a/platform_versioned_docs/version-24.3/data_studios/custom-envs.mdx +++ b/platform_versioned_docs/version-24.3/studios/custom-envs.mdx @@ -1,13 +1,13 @@ --- title: "Custom environments" -description: "Custom environments for Data Studios" +description: "Custom environments for Studios" date: "1 Oct 2024" tags: [data, studios] --- In addition to the Seqera-provided container template images, you can provide your own custom container environments by augmenting the Seqera-provided images with a list of Conda packages or by providing your own base container template image. -Data Studios uses the [Wave][wave-home] service to build custom container template images. +Studios uses the [Wave][wave-home] service to build custom container template images. ## Conda packages @@ -21,7 +21,7 @@ Data Studios uses the [Wave][wave-home] service to build custom container templa ### Conda package syntax {#conda-package-syntax} -When adding a new data studio session, you can customize its configuration to install a list of Conda packages to the template image. The supported schema is identical to that used by the Conda `environment.yml` file. For more information on the Conda environment file, see [Creating an environment file manually][env-manually]. +When adding a new Studio, you can customize its configuration to install a list of Conda packages to the template image. The supported schema is identical to that used by the Conda `environment.yml` file. For more information on the Conda environment file, see [Creating an environment file manually][env-manually]. ```yaml title="Example environment.yml file" channels: diff --git a/platform_versioned_docs/version-24.3/data_studios/index.mdx b/platform_versioned_docs/version-24.3/studios/index.mdx similarity index 81% rename from platform_versioned_docs/version-24.3/data_studios/index.mdx rename to platform_versioned_docs/version-24.3/studios/index.mdx index 55d721ed3..fd0c4d278 100644 --- a/platform_versioned_docs/version-24.3/data_studios/index.mdx +++ b/platform_versioned_docs/version-24.3/studios/index.mdx @@ -5,12 +5,12 @@ date: "6 February 2025" tags: [studios] --- -Studios is a unified platform where you can host a combination of container images and compute environments for interactive analysis using your preferred tools, like JupyterLab and RStudio Notebooks, Visual Studio Code IDEs, or Xpra remote desktops. Each Data Studio session is an individual interactive environment that encapsulates the live environment for dynamic data analysis. +Studios is a unified platform where you can host a combination of container images and compute environments for interactive analysis using your preferred tools, like JupyterLab and RStudio Notebooks, Visual Studio Code IDEs, or Xpra remote desktops. Each Studio session is an individual interactive environment that encapsulates the live environment for dynamic data analysis. On Seqera Cloud, the free tier permits only one running session at a time. To run simultaneous sessions, [contact Seqera][contact] for a Seqera Cloud Pro license. :::note -Data Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Data Studios in Enterprise is not enabled by default. You can enable Data Studios in the [environment variables configuration](../../version-24.2/enterprise/data-studios.mdx). +Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Data Studios in Enterprise is not enabled by default. You can enable Data Studios in the [environment variables configuration](../../version-24.2/enterprise/data-studios.mdx). ::: ## Requirements @@ -34,7 +34,7 @@ For more information on AWS Batch configuration, see [AWS Batch][aws-batch]. ## Container image templates -Data Studios provides four container image templates: JupyterLab, RStudio Server, Visual Studio Code, and Xpra. The image templates install a very limited number of packages when the session container is built. You can install additional packages as needed during a session. +Studios provides four container image templates: JupyterLab, RStudio Server, Visual Studio Code, and Xpra. The image templates install a very limited number of packages when the session container is built. You can install additional packages as needed during a session. The image template tag includes the version of the analysis application, an optional incompatibility flag, and the Seqera Connect version. Connect is the proprietary Seqera web server client that manages communication with the container. The tag string looks like this: @@ -113,15 +113,15 @@ To see the list of all Xpra image templates available, see [public.cr.seqera.io/ ## Session statuses -Data studios have the following possible statuses: +Studios have the following possible statuses: -- **building**: When a custom environment is building the template image for a new data studio session. The [Wave] service performs the build action. For more information on this status, see [Inspect custom container template build status][build-status]. +- **building**: When a custom environment is building the template image for a new Studio session. The [Wave] service performs the build action. For more information on this status, see [Inspect custom container template build status][build-status]. - **build-failed**: When a custom environment build has failed. This is a non-recoverable error. Logs are provided to assist with troubleshooting. For more information on this status, see [Inspect custom container template build status][build-status]. -- **starting**: The data studio is initializing. -- **running**: When a data studio session is **running**, you can connect to it, copy the data studio URL, or stop it. In addition, the session can continue to process requests/run computations in the absence of an ongoing connection. +- **starting**: The Studio is initializing. +- **running**: When a Studio session is **running**, you can connect to it, copy the URL, or stop it. In addition, the session can continue to process requests/run computations in the absence of an ongoing connection. - **stopping**: The recently-running session is in the process of being stopped. -- **stopped**: When a session is stopped, the associated compute resources are deallocated. You can start or delete the data studio when it's in this state. -- **errored**: This state most often indicates that there has been an error starting the data studio session but it is in a **stopped** state. There might be errors reported by the session itself but these will be overwritten with a **running** status if the data studio session is still running. +- **stopped**: When a session is stopped, the associated compute resources are deallocated. You can start or delete the Studio when it's in this state. +- **errored**: This state most often indicates that there has been an error starting the Studio session but it is in a **stopped** state. There might be errors reported by the session itself but these will be overwritten with a **running** status if the session is still running. :::tip If you encounter an error with the public preview release of Studios, [contact Seqera support][contact]. @@ -146,11 +146,11 @@ For more information, see [Limit Studio access to a specific cloud bucket subdir When starting a Studio session, a *checkpoint* is automatically created. A checkpoint saves all changes made to the root filesystem and stores it in the attached compute environment's pipeline work directory in the `.studios/checkpoints` folder with a unique name. The current checkpoint is updated every five minutes during a session. -When you stop and start a data studio session, or start a new data studio session from a previously created checkpoint, changes such as installed software packages and configuration files are restored and made available in the data studio session. Changes made to mounted data are not included in a checkpoint. +When you stop and start a Studio session, or start a new Studio session from a previously created checkpoint, changes such as installed software packages and configuration files are restored and made available in the Studio session. Changes made to mounted data are not included in a checkpoint. -Checkpoints can be renamed and the name has to be unique per data studio. Spaces in checkpoint names are converted to underscores automatically. +Checkpoints can be renamed and the name has to be unique per Studio. Spaces in checkpoint names are converted to underscores automatically. -Checkpoint files in the compute environment work directory may be shared by multiple data studios. Each checkpoint file is cleaned up asynchronously after the last data studio referencing the checkpoint is deleted. +Checkpoint files in the compute environment work directory may be shared by multiple data studios. Each checkpoint file is cleaned up asynchronously after the last Studio referencing the checkpoint is deleted. :::note The cleanup process is a best effort and not guaranteed. Seqera attempts to remove the checkpoint, but it can fail if, for example, the compute environment credentials used do not have sufficient permissions to delete objects from storage buckets. @@ -166,7 +166,7 @@ The maximum storage allocation for a session is limited by the compute environme If the maximum allocation size is reached, it is possible to reclaim storage space using a snapshot. -Stop the active session to trigger a snapshot from the active volume. Data Studios uploads the snapshot to cloud storage with Fusion. When you start from the newly saved snapshot, all previous data is loaded and the newly-started session will have 2 GB of available space. +Stop the active session to trigger a snapshot from the active volume. Studios uploads the snapshot to cloud storage with Fusion. When you start from the newly saved snapshot, all previous data is loaded and the newly-started session will have 2 GB of available space. {/* links */} [contact]: https://support.seqera.io/ diff --git a/platform_versioned_docs/version-24.3/data_studios/managing.mdx b/platform_versioned_docs/version-24.3/studios/managing.mdx similarity index 58% rename from platform_versioned_docs/version-24.3/data_studios/managing.mdx rename to platform_versioned_docs/version-24.3/studios/managing.mdx index 8a8c82f38..a65196ab3 100644 --- a/platform_versioned_docs/version-24.3/data_studios/managing.mdx +++ b/platform_versioned_docs/version-24.3/studios/managing.mdx @@ -1,19 +1,19 @@ --- -title: "Manage data studio sessions" -description: "Manage data studio sessions." +title: "Manage Studio sessions" +description: "Manage Studio sessions." date: "6 February 2025" tags: [data, studios] --- -Select the **Data Studios** tab in Platform to view all data studio sessions. The list includes the name, cloud provider, analysis template, region, author, creation date, and status of each session. In this view, you can add a new data studio and start, stop, or connect to an existing session. Dynamically filter the list of data studios using the search bar to search by name (default), author username, or compute environment name. Select the data studio to open a detailed view that displays configuration information. +Select the **Studios** tab in Platform to view all Studio sessions. The list includes the name, cloud provider, analysis template, region, author, creation date, and status of each session. In this view, you can add a new Studio and start, stop, or connect to an existing session. Dynamically filter the list of Studios using the search bar to search by name (default), author username, or compute environment name. Select a Studio to open a detailed view that displays configuration information. -## Add a data studio +## Add a Studio This functionality is available to users with the **Maintain** role and above. -To add a new data studio, complete the following steps: +To add a new Studio, complete the following steps: -1. In a workspace, select **Data Studios**, and then select **Add data studio**. +1. In a workspace, select **Studios**, and then select **Add Studio**. 1. For the **Compute & Data** section, complete the following steps: 1. Customize the following fields: @@ -35,7 +35,7 @@ To add a new data studio, complete the following steps: 1. Customize the following fields: - **Container template**: Select a data studio template from the dropdown list. - - **Data studio name** + - **Studio name** - Optional: **Description** 1. Optional: Select **Install Conda packages** to enter or upload a list of Conda packages to include with the data studio. For more information on the syntax for specifying Conda packages, see [Conda package syntax][conda-syntax]. 1. Select **Next**. @@ -56,69 +56,69 @@ To add a new data studio, complete the following steps: 1. For the **Summary** section, complete the following steps: 1. Ensure that the specified configuration is correct. 1. Save your configuration: - - If you want to save the data studio for future use, select **Add only**. - - If you want to save and immediately start the data studio, select **Add and start**. + - If you want to save the Studio for future use, select **Add only**. + - If you want to save and immediately start the Studio, select **Add and start**. -You'll be returned to the Data Studios landing page that displays the list of data studio sessions in your workspace. You can inspect the configuration details of the session that you created by selecting the session name. The data studio that you created will be listed with a status of either **stopped** or **starting**, depending on whether you elected to only add the data studio or to start a session as well. +You'll be returned to the Studios landing page that displays the list of Studio sessions in your workspace. You can inspect the configuration details of the session that you created by selecting the session name. The Studio that you created will be listed with a status of either **stopped** or **starting**, depending on whether you elected to only add it or to start a session as well. :::note -By default, data studio sessions only have read permissions to mounted data paths. Write permissions can be added for specific cloud storage buckets during the compute environment configuration by defining additional **Allowed S3 Buckets**. This means that data can be written from the session back to the cloud storage path(s) mounted. To stop potential data loss, only one session per workspace can mount a unique data path. When adding a new session, data paths already mounted to other running sessions are unavailable. If a new file is uploaded to the cloud storage bucket path while a session is running, the file may not be available to the session immediately. +By default, sessions only have read permissions to mounted data paths. Write permissions can be added for specific cloud storage buckets during the compute environment configuration by defining additional **Allowed S3 Buckets**. This means that data can be written from the session back to the cloud storage path(s) mounted. To stop potential data loss, only one session per workspace can mount a unique data path. When adding a new session, data paths already mounted to other running sessions are unavailable. If a new file is uploaded to the cloud storage bucket path while a session is running, the file may not be available to the session immediately. ::: -## Start a data studio session +## Start a Studio session This functionality is available to users with the **Maintain** role and above. -A data studio needs to be started before you can connect to it. From the list in your workspace, select the three dots next to the status message for the data studio you want to start, then select **Start**. You can optionally change the configuration of the data studio, then select **Start in new tab**. A new browser tab will open that displays the startup state of the data studio session. Once the session is running, you can connect to it. A session will run until it is stopped manually or it encounters a technical issue. +A Studio needs to be started before you can connect to it. Select the three dots next to the status message for the Studio you want to start, then select **Start**. You can optionally change the configuration of the Studio, then select **Start in new tab**. A new browser tab will open that displays the startup state of the session. Once the session is running, you can connect to it. A session will run until it is stopped manually or it encounters a technical issue. :::note -A data studio session consumes resources until it's **stopped**. +A session consumes resources until it's **stopped**. ::: Once a session is in a **running** state, you can connect to it, obtain the public link to the session to share with collaborators inside your workspace, and stop it. -## Start an existing data studio as a new session +## Start an existing Studio as a new session This functionality is available to users with the **Maintain** role and above. -You can use any existing data studio as the foundation for adding a new data studio. This functionality creates a clone of the data studio, including its checkpoint history, preserving any modifications made to the original data studio. When you create a session in this way, future changes are isolated from the original session. +You can use any existing Studio as the foundation for adding a new data studio. This functionality creates a clone of the Studio, including its checkpoint history, preserving any modifications made to the original Studio. When you create a session in this way, future changes are isolated from the original session. When adding a new session from an existing session or checkpoint, the following fields cannot be changed: -- **Data Studio Template** -- **Original data studio session and checkpoint** +- **Studio Template** +- **Original Studio session and checkpoint** - **Compute environment** - **Installed Conda packages** -To add a new session from an existing **stopped** session, complete the steps described in [Add a data studio](#add-a-data-studio). +To add a new session from an existing **stopped** session, complete the steps described in [Add a Studio](#add-a-studio). -Additionally, you can add a new session from any existing data studio checkpoint except the currently running checkpoint. From the data studio detail page, select the **Checkpoints** tab and in the **Actions** column, select **Start as new data studio**. This is useful for interactive analysis experimentation without impacting the state of the original data studio. +Additionally, you can add a new session from any existing Studio checkpoint except the currently running checkpoint. From the detail page, select the **Checkpoints** tab and in the **Actions** column, select **Start as new Studio**. This is useful for interactive analysis experimentation without impacting the state of the original Studio. -## Connect to a data studio +## Connect to a Studio This functionality is available to all user roles excluding the **View** role. -To connect to a running session, select the three dots next to the status message and choose **Connect**. A new browser tab will open containing the data studio session. +To connect to a running session, select the three dots next to the status message and choose **Connect**. :::warning An active connection to a session will not prevent administrative actions that might disrupt that connection. For example, a session can be stopped by another workspace user while you are active in the session, the underlying credentials can be changed, or the compute environment can be deleted. These are independent actions and the user in the session won't be alerted to any changes - the only alert will be a server connection error in the active session browser tab. ::: -Once connected, the data studio session will display the status of **running** in the list, and any connected user's avatar will be displayed under the status in both the list of data studios and in each data studio session detail page. +Once connected, the session will display the status of **running** in the list, and any connected user's avatar will be displayed under the status in both the list of data studios and in each Studio's detail page. -## Collaborate in a data studio +## Collaborate in a Studio This functionality is available to all user roles excluding the **View** role. -To share a link to a running session with collaborators inside your workspace, select the three dots next to the status message for the session you want to share, then select **Copy data studio URL**. Using this link, other authenticated users can access the session directly. +To share a link to a running session with collaborators inside your workspace, select the three dots next to the status message for the session you want to share, then select **Copy Studio URL**. Using this link, other authenticated users can access the session directly. -![](../data/_images/data_studios_collaboration.png) +![](../data/_images/studios_collaboration.png) :::note -Collaborators need valid workspace permissions to connect to the running data studio. +Collaborators need valid workspace permissions to connect to the running Studio. ::: -## Stop a data studio +## Stop a Studio This functionality is available to users with the **Maintain** role and above. @@ -126,7 +126,7 @@ To stop a running session, select the three dots next to the status message and Stopping a running session creates a new checkpoint. -## Restart a stopped data studio +## Restart a stopped Studio This functionality is available to users with the **Maintain** role and above. @@ -136,9 +136,9 @@ When you restart a stopped session, the session uses the most recent checkpoint. This functionality is available to users with the **Maintain** role and above. -You can start a new session from an existing stopped session. This will inherit the history of the parent checkpoint state. From the list of **stopped** data studios in your workspace, select the three dots next to the status message for the data studio and select **Start as new**. Alternatively, select the **Checkpoints** tab on the data studio detail page, select the three dots in the **Actions** column, and then select **Start as new** to start a new session. +You can start a new session from an existing stopped session. This will inherit the history of the parent checkpoint state. From the list of **stopped** Studios in your workspace, select the three dots next to the status message for the data studio and select **Start as new**. Alternatively, select the **Checkpoints** tab on the detail page, select the three dots in the **Actions** column, and then select **Start as new** to start a new session. -## Delete a data studio session +## Delete a Studio session This functionality is available to users with the **Maintain** role and above. diff --git a/platform_versioned_sidebars/version-24.3-sidebars.json b/platform_versioned_sidebars/version-24.3-sidebars.json index 59b783a12..07719e0c5 100644 --- a/platform_versioned_sidebars/version-24.3-sidebars.json +++ b/platform_versioned_sidebars/version-24.3-sidebars.json @@ -117,11 +117,11 @@ }, { "type": "category", - "label": "Data Studios", + "label": "Studios", "items": [ - "data_studios/index", - "data_studios/custom-envs", - "data_studios/managing" + "studios/index", + "studios/custom-envs", + "studios/managing" ] }, { diff --git a/static/_redirects b/static/_redirects index b18862539..47b875c9c 100644 --- a/static/_redirects +++ b/static/_redirects @@ -27,6 +27,11 @@ /platform/24.1/data/data-studios /platform/latest/data_studios/ 301 /platform/24.2/data/data-studios /platform/latest/data_studios/ 301 +# Redirect all Data Studios content to Studios +/platform/24.1/data/data-studios /platform/latest/studios/ 301 +/platform/24.2/data/data-studios /platform/latest/studios/ 301 +/platform/latest/data-studios/* /platform/latest/studios/* 301 + # Redirect first result on Google for CLI docs /platform/23.3/cli /platform/latest/cli/overview/:splat 301 From 5350744d1e5ae09c85992226663eb125bc75ff16 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Mon, 17 Feb 2025 23:50:39 +0200 Subject: [PATCH 04/30] Renaming images --- .../_images/studios_collaboration.png} | Bin .../_images/studios_notebook_fusion.png} | Bin .../version-24.3/studios/custom-envs.mdx | 4 ++-- .../version-24.3/studios/managing.mdx | 2 +- 4 files changed, 3 insertions(+), 3 deletions(-) rename platform_versioned_docs/version-24.3/{data/_images/data_studios_collaboration.png => studios/_images/studios_collaboration.png} (100%) rename platform_versioned_docs/version-24.3/{data/_images/data_studios_notebook_fusion.png => studios/_images/studios_notebook_fusion.png} (100%) diff --git a/platform_versioned_docs/version-24.3/data/_images/data_studios_collaboration.png b/platform_versioned_docs/version-24.3/studios/_images/studios_collaboration.png similarity index 100% rename from platform_versioned_docs/version-24.3/data/_images/data_studios_collaboration.png rename to platform_versioned_docs/version-24.3/studios/_images/studios_collaboration.png diff --git a/platform_versioned_docs/version-24.3/data/_images/data_studios_notebook_fusion.png b/platform_versioned_docs/version-24.3/studios/_images/studios_notebook_fusion.png similarity index 100% rename from platform_versioned_docs/version-24.3/data/_images/data_studios_notebook_fusion.png rename to platform_versioned_docs/version-24.3/studios/_images/studios_notebook_fusion.png diff --git a/platform_versioned_docs/version-24.3/studios/custom-envs.mdx b/platform_versioned_docs/version-24.3/studios/custom-envs.mdx index 90b336431..3a1c41936 100644 --- a/platform_versioned_docs/version-24.3/studios/custom-envs.mdx +++ b/platform_versioned_docs/version-24.3/studios/custom-envs.mdx @@ -109,8 +109,8 @@ If the custom container template image build fails, the data studio session has To inspect the status of an ongoing build, or a successful or failed build, complete the following steps: -1. Select the **Data Studios** tab in Seqera Platform. -1. From the list of data studio sessions, select the name of the session with **building** or **build-failed** status that you want to inspect, and then select **View**. +1. Select the **Studios** tab in Seqera Platform. +1. From the list of sessions, select the name of the session with **building** or **build-failed** status that you want to inspect, and then select **View**. 1. In the **Details** tab, scroll to **Build reports** and select **Summary** to open the Wave service container build report for your build. 1. Optional: If the build failed, select the **Error report** tab to view the errors associated with the build failure. diff --git a/platform_versioned_docs/version-24.3/studios/managing.mdx b/platform_versioned_docs/version-24.3/studios/managing.mdx index a65196ab3..2c99ac4c9 100644 --- a/platform_versioned_docs/version-24.3/studios/managing.mdx +++ b/platform_versioned_docs/version-24.3/studios/managing.mdx @@ -112,7 +112,7 @@ This functionality is available to all user roles excluding the **View** role. To share a link to a running session with collaborators inside your workspace, select the three dots next to the status message for the session you want to share, then select **Copy Studio URL**. Using this link, other authenticated users can access the session directly. -![](../data/_images/studios_collaboration.png) +![](./_images/studios_collaboration.png) :::note Collaborators need valid workspace permissions to connect to the running Studio. From b1635774f3d60abfd4f946ce1080d10d7104b131 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Mon, 17 Feb 2025 23:55:00 +0200 Subject: [PATCH 05/30] Minor fixes --- .../{studios => data_studios}/custom-envs.mdx | 2 +- .../version-24.2/studios/index.mdx | 163 ------------------ .../version-24.2/studios/managing.mdx | 152 ---------------- .../version-24.3/studios/custom-envs.mdx | 4 +- .../version-24.3/studios/managing.mdx | 2 +- 5 files changed, 4 insertions(+), 319 deletions(-) rename platform_versioned_docs/version-24.2/{studios => data_studios}/custom-envs.mdx (98%) delete mode 100644 platform_versioned_docs/version-24.2/studios/index.mdx delete mode 100644 platform_versioned_docs/version-24.2/studios/managing.mdx diff --git a/platform_versioned_docs/version-24.2/studios/custom-envs.mdx b/platform_versioned_docs/version-24.2/data_studios/custom-envs.mdx similarity index 98% rename from platform_versioned_docs/version-24.2/studios/custom-envs.mdx rename to platform_versioned_docs/version-24.2/data_studios/custom-envs.mdx index 8fad711df..5b4bc2ce0 100644 --- a/platform_versioned_docs/version-24.2/studios/custom-envs.mdx +++ b/platform_versioned_docs/version-24.2/data_studios/custom-envs.mdx @@ -33,7 +33,7 @@ dependencies: - seaborn ``` -To create a data studio with custom Conda packages, see [Add a data studio][add-ds]. +To create a Studio with custom Conda packages, see [Add a Studio][add-s]. ## Custom container template image {#custom-containers} diff --git a/platform_versioned_docs/version-24.2/studios/index.mdx b/platform_versioned_docs/version-24.2/studios/index.mdx deleted file mode 100644 index cc548ad04..000000000 --- a/platform_versioned_docs/version-24.2/studios/index.mdx +++ /dev/null @@ -1,163 +0,0 @@ ---- -title: "Overview" -description: "Studios public preview." -date: "1 Oct 2024" -tags: [data, studios] ---- - -Studios is a unified platform where you can host a combination of container images and compute environments for interactive analysis using your preferred tools, like JupyterLab and RStudio Notebooks, Visual Studio Code IDEs, or Xpra remote desktops. Each Studio is an individual interactive environment that encapsulates the live environment for dynamic data analysis. - -On Seqera Cloud, the free tier permits only one running session at a time. To run simultaneous sessions, [contact Seqera][contact] for a Seqera Cloud Pro license. - -:::note -Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Studios in Enterprise is not enabled by default. You can enable it in the [environment variables configuration](../enterprise/studios.mdx). -::: - -## Requirements - -Before you get started, you need the following: - -- Valid credentials to access your cloud storage data resources. -- At minimum the **Maintain** role set of permissions. -- A compute environment with sufficient resources. This is highly dependent on the volume of data you wish to process, but we recommended at least 2 CPUs allocated with 8192 MB of memory. See [AWS Batch](../compute-envs/aws-batch.mdx) for more information about compute environment configuration. -- [Data Explorer](../data/data-explorer.mdx) is enabled. - -:::note -Currently, Studios only supports AWS Batch compute environments that **do not** have Fargate enabled. -::: - -## Limitations - -If you configured your AWS Batch compute environment to include an EFS file system with **EFS file system > EFS mount path**, the mount path must be explicitly specified. The mount path cannot be the same as your compute environment work directory. If the EFS file system is mounted as your compute environment work directory, snapshots cannot be saved and sessions fail. To mount an EFS volume in a studio session (for example, if your organization has a custom, managed, and standardized software stack in an EFS volume), add the EFS volume to the compute environment (system ID and mount path). The volume will be available at the specified mount path in the session. - -For more information on AWS Batch configuration, see [AWS Batch][aws-batch]. - -## Container image templates - -Studios provides four container image templates: JupyterLab, RStudio Server, Visual Studio Code, and Xpra. The image templates install a very limited number of packages when the session container is built. You can install additional packages as needed during a session. - -The image template tag includes the version of the analysis application, an optional incompatibility flag, and the Seqera Connect version. Connect is the proprietary Seqera web server client that manages communication with the container. The tag string looks like this: - -```ignore title="Image template tag" --[u]- -``` - -- ``: Third-party analysis application that follows its own semantic versioning `..`, such as `4.2.5` for JupyterLab. -- ``: Optional analysis application update version, such as `u1`, for instances where a backwards incompatible change is introduced. -- ``: Seqera Connect client version, such as `0.7` or `0.7.0`. - -Additionally, the Seqera Connect client version string has the format: - -```ignore title="Seqera version tag subset" -.. -``` - -- ``: Signifies major version changes in the underlying Seqera Connect client. -- ``: Signifies breaking changes in the underlying Seqera Connect client. -- ``: Signifies patch (non-breaking) changes in the underlying Seqera Connect client. - -When pushed to the container registry, an image template is tagged with the following tags: - -- `-.`, such as `4.2.3-0.7`. When adding a new data studio container template image this is the tag displayed in Seqera Platform. -- `-..`, such as `4.2.3-0.7.1`. - -To view the latest versions of the images, see [public.cr.seqera.io](https://public.cr.seqera.io/). You can also augment the Seqera-provided image templates or use your own custom container image templates. This approach is recommended for managing reproducible analysis environments. For more information, see [Custom environments][custom-envs]. - -**JupyterLab 4.2.5** - -The default user is the `root` account. The following [conda-forge](https://conda-forge.org/) packages are available by default: - -- `python=3.13.0` -- `pip=24.2` -- `jedi-language-server=0.41.4` -- `jupyterlab=4.2.5` -- `jupyter-collaboration=1.2.0` -- `jupyterlab-git=0.50.1` -- `jupytext=1.16.4` -- `jupyter-dash=0.4.2` -- `ipywidgets=7.8.4` -- `pandas[all]=2.2.3` -- `scikit-learn=1.5.2` -- `statsmodels=0.14.4` -- `itables=2.2.2` -- `seaborn[stats]=0.13.2` -- `altair=5.4.1` -- `plotly=5.24.1` -- `r-ggplot2=3.5.1` -- `nb_black=1.0.7` -- `qgrid=1.3.1` - -To install additional Python packages during a running session, execute `!pip install ` commands in your notebook environment. Additional system-level packages can be installed in a terminal window using `apt install `. - -To see the list of all JupyterLab image templates available, see [public.cr.seqera.io/repo/platform/data-studio-jupyter](https://public.cr.seqera.io/repo/platform/data-studio-jupyter). - -**RStudio Server 4.4.1** - -The default user is the `root` account. To install R packages during a running session, execute `install.packages("")` commands in your notebook environment. Additional system-level packages can be installed in a terminal window using `apt install `. - -To see the list of all RStudio Server image templates available, see [public.cr.seqera.io/repo/platform/data-studio-rstudio](https://public.cr.seqera.io/repo/platform/data-studio-rstudio). - -**Visual Studio Code 1.93.1** - -[Visual Studio Code][vsc] is an integrated development environment (IDE) that supports many programming languages. The default user is the `root` account. To install extensions during a running session, select **Extensions**. Additional system-level packages can be installed in a terminal window using `apt install `. - -To see the list of all Visual Studio Code image templates available, see [public.cr.seqera.io/platform/data-studio-vscode](https://public.cr.seqera.io/repo/platform/data-studio-vscode). - -**Xpra 6.2.0** - -[Xpra](https://github.com/Xpra-org/xpra), known as _screen for X_, allows you to run X11 programs by giving you remote access to individual graphical applications. The container template image also installs NVIDIA Linux x64 (AMD64/EM64T) drivers for Ubuntu 22.04 for running GPU-enabled applications. To use these GPU drivers, your compute environment must specify GPU instance families. - -The default user is the `root` account. The image is based on `ubuntu:jammy`. Additional system-level packages can be installed during a running session in a terminal window using `apt install `. - -To see the list of all Xpra image templates available, see [public.cr.seqera.io/repo/platform/data-studio-xpra](https://public.cr.seqera.io/repo/platform/data-studio-xpra). - -## Session statuses - -Data studios have the following possible statuses: - -- **building**: When a custom environment is building the template image for a new Studio. The [Wave] service performs the build action. For more information on this status, see [Inspect custom container template build status][build-status]. -- **build-failed**: When a custom environment build has failed. This is a non-recoverable error. Logs are provided to assist with troubleshooting. For more information on this status, see [Inspect custom container template build status][build-status]. -- **starting**: The data studio is initializing. -- **running**: When a data studio session is **running**, you can connect to it, copy the data studio URL, or stop it. In addition, the session can continue to process requests/run computations in the absence of an ongoing connection. -- **stopping**: The recently-running session is in the process of being stopped. -- **stopped**: When a session is stopped, the associated compute resources are deallocated. You can start or delete the data studio when it's in this state. -- **errored**: This state most often indicates that there has been an error starting the data studio session but it is in a **stopped** state. There might be errors reported by the session itself but these will be overwritten with a **running** status if the data studio session is still running. - - :::tip - If you encounter an error with the public preview release of Data Studios, [contact Seqera support][contact]. - ::: - -## Session checkpoints - -When you start a session, it automatically creates a *checkpoint*. A checkpoint saves changes that you make to the root filesystem and stores it in the compute environment's pipeline work directory in the `.studios/checkpoints` folder with a unique name. The checkpoint is updated every five minutes. - -When you stop and start a data studio session, or start a new data studio session from a previously created checkpoint, changes such as installed software packages and configuration files are restored and made available in the data studio session. Changes made to mounted data are not included in a checkpoint. - -Checkpoints can be renamed and the name has to be unique per data studio. Spaces in checkpoint names are converted to underscores automatically. - -Checkpoint files in the compute environment work directory may be shared by multiple data studios. Each checkpoint file is cleaned up asynchronously after the last data studio referencing the checkpoint is deleted. - -:::note -The cleanup process is a best effort and not guaranteed. Seqera attempts to remove the checkpoint, but it can fail if, for example, the compute environment credentials used do not have sufficient permissions to delete objects from storage buckets. -::: - -## Session volume automatic resizing - -By default, a session allocates an initial 2 GB of storage. Available disk space is continually monitored and if the available space drops below a 1 GB threshold, the file system is dynamically-resized to include an additional 2 GB of available disk space. - -This approach ensures that a session doesn't initially include unnecessary free disk space, while providing the flexibility to accommodate installation of large software packages required for data analysis. - -The maximum storage allocation for a session is limited by the compute environment disk boot size. By default, this is 30 GB. This limit is shared by all sessions running in the same compute environment. - -If the maximum allocation size is reached, it is possible to reclaim storage space using a snapshot. - -Stop the active session to trigger a snapshot from the active volume. Data Studios uploads the snapshot to cloud storage with Fusion. When you start from the newly saved snapshot, all previous data is loaded and the newly-started session will have 2 GB of available space. - - -[contact]: https://support.seqera.io/ -[vsc]: https://code.visualstudio.com/ -[Wave]: https://seqera.io/wave/ - -[aws-batch]: ../compute-envs/aws-batch.mdx -[custom-envs]: ./custom-envs.mdx -[build-status]: ./custom-envs.mdx#build-status diff --git a/platform_versioned_docs/version-24.2/studios/managing.mdx b/platform_versioned_docs/version-24.2/studios/managing.mdx deleted file mode 100644 index 8b7859d0a..000000000 --- a/platform_versioned_docs/version-24.2/studios/managing.mdx +++ /dev/null @@ -1,152 +0,0 @@ ---- -title: "Manage data studio sessions" -description: "Manage data studio sessions." -date: "1 Oct 2024" -tags: [data, studios] ---- - -Select the **Data Studios** tab in Platform to view all data studio sessions. The list includes the name, cloud provider, analysis template, region, author, creation date, and status of each session. In this view, you can add a new data studio and start, stop, or connect to an existing session. Dynamically filter the list of data studios using the search bar to search by name (default), author username, or compute environment name. Select the data studio to open a detailed view that displays configuration information. - -## Add a data studio - -This functionality is available to users with the **Maintain** role and above. - -To add a new data studio, complete the following steps: - -1. In a workspace, select **Data Studios**, and then select **Add data studio**. -1. For the **Compute & Data** section, complete the following steps: - - 1. Customize the following fields: - - **Select compute environment**: Only AWS Batch is supported. - - **CPUs allocated**: The default allocation is 2 CPUs. - - **GPUs allocated**: Available only if the selected compute environment has GPU support enabled. For more information about GPUs on AWS, see [Amazon ECS task definitions for GPU workloads][aws-gpu]. The default allocation is 0 GPUs. - - **Maximum memory allocated**: The default allocation is 8192 MiB of memory. - 1. Select **Mount data**, and then from the **Mount data** modal, select data to mount. Select **Mount data** to confirm your selection. - - :::tip - Datasets are mounted using the [Fusion file system](https://docs.seqera.io/fusion) and are available at `/workspace/data/`. Mounted data doesn't need to match the compute environment or region of the cloud provider of the data studio. However, this might cause increased costs or errors. - ::: - - 1. Select **Next**. - -1. For the **General config** section, complete the following steps: - - - To use one of the Seqera-provided container templates, complete the following steps: - - 1. Customize the following fields: - - **Container template**: Select a data studio template from the dropdown list. - - **Data studio name** - - Optional: **Description** - 1. Optional: Select **Install Conda packages** to enter or upload a list of Conda packages to include with the data studio. For more information on the syntax for specifying Conda packages, see [Conda package syntax][conda-syntax]. - 1. Select **Next**. - - - To use a custom container template image that you supply, complete the following steps: - - 1. Customize the following fields: - - **Container template**: Select **Prebuilt container image** from the list. For information about providing your own template, see [Custom container template image][custom-image]. - - :::tip - If you select the **Prebuilt container image** template, you cannot select **Install Conda packages** as these options are mutually exclusive. - ::: - - - **Data studio name** - - Optional: **Description** - 1. Select **Next**. - -1. For the **Summary** section, complete the following steps: - 1. Ensure that the specified configuration is correct. - 1. Save your configuration: - - If you want to save the data studio for future use, select **Add only**. - - If you want to save and immediately start the data studio, select **Add and start**. - -You'll be returned to the Data Studios landing page that displays the list of data studio sessions in your workspace. You can inspect the configuration details of the session that you created by selecting the session name. The data studio that you created will be listed with a status of either **stopped** or **starting**, depending on whether you elected to only add the data studio or to start a session as well. - -:::note -By default, data studio sessions only have read permissions to mounted data paths. Write permissions can be added for specific cloud storage buckets during the compute environment configuration by defining additional **Allowed S3 Buckets**. This means that data can be written from the session back to the cloud storage path(s) mounted. To stop potential data loss, only one session per workspace can mount a unique data path. When adding a new session, data paths already mounted to other running sessions are unavailable. If a new file is uploaded to the cloud storage bucket path while a session is running, the file may not be available to the session immediately. -::: - -## Start a data studio session - -This functionality is available to users with the **Maintain** role and above. - -A data studio needs to be started before you can connect to it. From the list in your workspace, select the three dots next to the status message for the data studio you want to start, then select **Start**. You can optionally change the configuration of the data studio, then select **Start in new tab**. A new browser tab will open that displays the startup state of the data studio session. Once the session is running, you can connect to it. A session will run until it is stopped manually or it encounters a technical issue. - -:::note -A data studio session consumes resources until it's **stopped**. -::: - -Once a session is in a **running** state, you can connect to it, obtain the public link to the session to share with collaborators inside your workspace, and stop it. - -## Start an existing data studio as a new session - -This functionality is available to users with the **Maintain** role and above. - -You can use any existing data studio as the foundation for adding a new data studio. This functionality creates a clone of the data studio, including its checkpoint history, preserving any modifications made to the original data studio. When you create a session in this way, future changes are isolated from the original session. - -When adding a new session from an existing session or checkpoint, the following fields cannot be changed: - -- **Data Studio Template** -- **Original data studio session and checkpoint** -- **Compute environment** -- **Installed Conda packages** - -To add a new session from an existing **stopped** session, complete the steps described in [Add a data studio](#add-a-data-studio). - -Additionally, you can add a new session from any existing data studio checkpoint except the currently running checkpoint. From the data studio detail page, select the **Checkpoints** tab and in the **Actions** column, select **Start as new data studio**. This is useful for interactive analysis experimentation without impacting the state of the original data studio. - -## Connect to a data studio - -This functionality is available to all user roles excluding the **View** role. - -To connect to a running session, select the three dots next to the status message and choose **Connect**. A new browser tab will open containing the data studio session. - -:::warning -An active connection to a session will not prevent administrative actions that might disrupt that connection. For example, a session can be stopped by another workspace user while you are active in the session, the underlying credentials can be changed, or the compute environment can be deleted. These are independent actions and the user in the session won't be alerted to any changes - the only alert will be a server connection error in the active session browser tab. -::: - -Once connected, the data studio session will display the status of **running** in the list, and any connected user's avatar will be displayed under the status in both the list of data studios and in each data studio session detail page. - -## Collaborate in a data studio - -This functionality is available to all user roles excluding the **View** role. - -To share a link to a running session with collaborators inside your workspace, select the three dots next to the status message for the session you want to share, then select **Copy data studio URL**. Using this link, other authenticated users can access the session directly. - -![](../data/_images/data_studios_collaboration.png) - -:::note -Collaborators need valid workspace permissions to connect to the running data studio. -::: - -## Stop a data studio - -This functionality is available to users with the **Maintain** role and above. - -To stop a running session, select the three dots next to the status message and then select **Stop**. The status will change from **running** to **stopped**. When a session is stopped, the compute resources it's using are deallocated. You can stop a session at any time, except when it is **starting**. - -Stopping a running session creates a new checkpoint. - -## Restart a stopped data studio - -This functionality is available to users with the **Maintain** role and above. - -When you restart a stopped session, the session uses the most recent checkpoint. - -## Start a new session from a checkpoint - -This functionality is available to users with the **Maintain** role and above. - -You can start a new session from an existing stopped session. This will inherit the history of the parent checkpoint state. From the list of **stopped** data studios in your workspace, select the three dots next to the status message for the data studio and select **Start as new**. Alternatively, select the **Checkpoints** tab on the data studio detail page, select the three dots in the **Actions** column, and then select **Start as new** to start a new session. - -## Delete a data studio session - -This functionality is available to users with the **Maintain** role and above. - -You can only delete a data studio when it's **stopped**. Select the three dots next to the status message and then select **Delete**. The data studio is deleted immediately and can't be recovered. - - - -[aws-gpu]: https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-gpu.html - -[conda-syntax]: ./custom-envs.mdx#conda-package-syntax -[custom-image]: ./custom-envs.mdx#custom-containers diff --git a/platform_versioned_docs/version-24.3/studios/custom-envs.mdx b/platform_versioned_docs/version-24.3/studios/custom-envs.mdx index 3a1c41936..a657b0b70 100644 --- a/platform_versioned_docs/version-24.3/studios/custom-envs.mdx +++ b/platform_versioned_docs/version-24.3/studios/custom-envs.mdx @@ -115,8 +115,8 @@ To inspect the status of an ongoing build, or a successful or failed build, comp 1. Optional: If the build failed, select the **Error report** tab to view the errors associated with the build failure. - -[add-ds]: ./managing.mdx#add-a-data-studio +{/* links */} +[add-s]: ./managing.mdx#add-a-studio [wave]: ../../version-24.2/enterprise/configuration/wave.mdx [wave-home]: https://seqera.io/wave/ diff --git a/platform_versioned_docs/version-24.3/studios/managing.mdx b/platform_versioned_docs/version-24.3/studios/managing.mdx index 2c99ac4c9..58abb0cf2 100644 --- a/platform_versioned_docs/version-24.3/studios/managing.mdx +++ b/platform_versioned_docs/version-24.3/studios/managing.mdx @@ -163,7 +163,7 @@ To limit read-write access to a specific subdirectory, complete the following st When defining a new Studio session, you can configure the **Mounted data** by selecting the custom data-link created by the previous steps. - +{/* links */} [aws-gpu]: https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ecs-gpu.html [conda-syntax]: ./custom-envs.mdx#conda-package-syntax From e94f72e38eb14cd627f096cc172e76d7ddc65a5f Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 18 Feb 2025 00:19:08 +0200 Subject: [PATCH 06/30] Studios --- .../version-24.3/cli/commands.mdx | 2 +- .../_images/{add-ds-pf.gif => add-s-pf.gif} | Bin .../getting-started/proteinfold.mdx | 20 ++++---- ...checkpoints.png => studio-checkpoints.png} | Bin ...-jupyter.gif => studio-create-jupyter.gif} | Bin ...ng => studio-jupyter-notebook-example.png} | Bin ...dios-overview.png => studios-overview.png} | Bin .../quickstart-demo/comm-showcase.mdx | 28 +++++------ .../{data-studios.mdx => studios.mdx} | 44 +++++++++--------- .../version-24.3/monitoring/dashboard.mdx | 8 ++-- 10 files changed, 51 insertions(+), 51 deletions(-) rename platform_versioned_docs/version-24.3/getting-started/_images/{add-ds-pf.gif => add-s-pf.gif} (100%) rename platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/{data-studio-checkpoints.png => studio-checkpoints.png} (100%) rename platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/{data-studio-create-jupyter.gif => studio-create-jupyter.gif} (100%) rename platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/{data-studio-jupyter-notebook-example.png => studio-jupyter-notebook-example.png} (100%) rename platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/{data-studios-overview.png => studios-overview.png} (100%) rename platform_versioned_docs/version-24.3/getting-started/quickstart-demo/{data-studios.mdx => studios.mdx} (55%) diff --git a/platform_versioned_docs/version-24.3/cli/commands.mdx b/platform_versioned_docs/version-24.3/cli/commands.mdx index 42a1d91fc..02101a162 100644 --- a/platform_versioned_docs/version-24.3/cli/commands.mdx +++ b/platform_versioned_docs/version-24.3/cli/commands.mdx @@ -272,7 +272,7 @@ https://api.cloud.seqera.io/workspaces/97652229034xxx/datasets/6vBGj6aWWpBuLpGKj Run `tw studios -h` to view the list of supported operations. -Manage [Studio sessions](../data_studios/index.mdx) hosted in Seqera Platform. Studio sessions allow interactive analysis using Jupyter, RStudio, VSCode, and Xpra. Additional custom analysis environments can be defined as needed. +Manage [Studio sessions](../studios/index.mdx) hosted in Seqera Platform. Studio sessions allow interactive analysis using Jupyter, RStudio, VSCode, and Xpra. Additional custom analysis environments can be defined as needed. :::note Most Studio operations require workspace `MAINTAIN` permissions. diff --git a/platform_versioned_docs/version-24.3/getting-started/_images/add-ds-pf.gif b/platform_versioned_docs/version-24.3/getting-started/_images/add-s-pf.gif similarity index 100% rename from platform_versioned_docs/version-24.3/getting-started/_images/add-ds-pf.gif rename to platform_versioned_docs/version-24.3/getting-started/_images/add-s-pf.gif diff --git a/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx b/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx index 598ff09e3..4f44a2c31 100644 --- a/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx +++ b/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx @@ -236,7 +236,7 @@ Specify your pipeline input and output and modify other pipeline parameters as n ![Mode options](./_images/proteinfold-mode.gif) :::info -For the purposes of this guide, run the pipeline in both `alphafold2` and `colabfold` modes. Specify unique directory paths for the `outdir` parameter (such as "Alphafold2" and "ColabFold") to ensure output data is kept separate and not overwritten. Predicted protein structures for each model will be visualized side-by-side in the [Interactive analysis](#interactive-analysis-with-data-studios) section. +For the purposes of this guide, run the pipeline in both `alphafold2` and `colabfold` modes. Specify unique directory paths for the `outdir` parameter (such as "Alphafold2" and "ColabFold") to ensure output data is kept separate and not overwritten. Predicted protein structures for each model will be visualized side-by-side in the [Interactive analysis](#interactive-analysis-with-studios) section. ::: ### Advanced settings @@ -306,19 +306,19 @@ After you have filled the necessary launch details, select **Launch**. The **Run -## Interactive analysis with Data Studios +## Interactive analysis with Studios -[Data Studios](../data_studios/index.mdx) streamlines the process of creating interactive analysis environments for Platform users. With built-in templates for platforms like Jupyter Notebook, RStudio, and VSCode, creating a data studio is as simple as adding and sharing pipelines or datasets. The data studio URL can also be shared with any user with the [Connect role](../orgs-and-teams/roles.mdx) for real-time access and collaboration. +[Studios](../studios/index.mdx) streamlines the process of creating interactive analysis environments for Platform users. With built-in templates for platforms like Jupyter Notebook, RStudio, and VSCode, creating a data studio is as simple as adding and sharing pipelines or datasets. The Studio URL can also be shared with any user with the [Connect role](../orgs-and-teams/roles.mdx) for real-time access and collaboration. For the purposes of this guide, a Jupyter notebook environment will be used for interactive visualization of the predicted protein structures, optionally comparing AlphaFold2 and Colabfold structures for the same sequence data. -### Create a Jupyter notebook data studio +### Create a Jupyter notebookStudio -From the **Data Studios** tab, select **Add a data studio** and complete the following: +From the **Studios** tab, select **Add a Studio** and complete the following: - In the **Compute & Data** tab: - Select your AWS Batch compute environment. :::info - The same compute environment can be used for pipeline execution and running your Data Studios notebook environment, but Data Studios does not support AWS Fargate and data studio sessions must run on CPUs. To use one compute environment for both nf-core/proteinfold execution and your data studio, leave **Enable Fargate for head job** disabled and include at least one CPU-based EC2 instance family (`c6id`, `r6id`, etc.) in your **Instance types**. + The same compute environment can be used for pipeline execution and running your Studios notebook environment, but Studios does not support AWS Fargate and data studio sessions must run on CPUs. To use one compute environment for both nf-core/proteinfold execution and your Studio, leave **Enable Fargate for head job** disabled and include at least one CPU-based EC2 instance family (`c6id`, `r6id`, etc.) in your **Instance types**. Alternatively, create a second basic AWS Batch compute environment with at least 2 CPUs and 8192 MB of RAM for your data studio. ::: @@ -343,11 +343,11 @@ From the **Data Studios** tab, select **Add a data studio** and complete the fol - conda-forge::ipywidgets=8.1.5 ``` -- Confirm the data studio details in the **Summary** tab -- Select **Add** and choose whether to add and start the studio immediately. -- When the data studio is created and in a running state, **Connect** to it. +- Confirm the Studio details in the **Summary** tab +- Select **Add** and choose whether to add and start the Studio immediately. +- When the Studio is created and in a running state, **Connect** to it. -![Add data studio](./_images/add-ds-pf.gif) +![Add Studio](./_images/add-s-pf.gif) ### Visualize protein structures diff --git a/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/data-studio-checkpoints.png b/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/studio-checkpoints.png similarity index 100% rename from platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/data-studio-checkpoints.png rename to platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/studio-checkpoints.png diff --git a/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/data-studio-create-jupyter.gif b/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/studio-create-jupyter.gif similarity index 100% rename from platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/data-studio-create-jupyter.gif rename to platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/studio-create-jupyter.gif diff --git a/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/data-studio-jupyter-notebook-example.png b/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/studio-jupyter-notebook-example.png similarity index 100% rename from platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/data-studio-jupyter-notebook-example.png rename to platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/studio-jupyter-notebook-example.png diff --git a/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/data-studios-overview.png b/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/studios-overview.png similarity index 100% rename from platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/data-studios-overview.png rename to platform_versioned_docs/version-24.3/getting-started/quickstart-demo/assets/studios-overview.png diff --git a/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/comm-showcase.mdx b/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/comm-showcase.mdx index d0abc87a5..1bf4345ad 100644 --- a/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/comm-showcase.mdx +++ b/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/comm-showcase.mdx @@ -13,7 +13,7 @@ import TabItem from '@theme/TabItem'; This demo tutorial provides an introduction to Seqera Platform, including instructions to: - Launch, monitor, and optimize the [nf-core/rnaseq](https://github.com/nf-core/rnaseq) pipeline - Select pipeline input data with [Data Explorer](../../data/data-explorer.mdx) and Platform [datasets](../../data/datasets.mdx) -- Perform interactive analysis of pipeline results with [Data Studios](../../data_studios/index.mdx) +- Perform interactive analysis of pipeline results with [Studios](../../studios/index.mdx) The Platform Community Showcase is a Seqera-managed demonstration workspace with all the resources needed to follow along with this tutorial. All [Seqera Cloud](https://cloud.seqera.io) users have access to this example workspace by default. ::: @@ -231,28 +231,28 @@ If a task fails, a good place to begin troubleshooting is the task's work direct Interactive analysis of pipeline results is often performed in platforms like Jupyter Notebook or RStudio. Setting up the infrastructure for these platforms, including accessing pipeline data and the necessary bioinformatics packages, can be complex and time-consuming. -**Data Studios** streamlines the process of creating interactive analysis environments for Platform users. With built-in templates, creating a data studio is as simple as adding and sharing pipelines or datasets. +**Studios** streamlines the process of creating interactive analysis environments for Platform users. With built-in templates, creating a data studio is as simple as adding and sharing pipelines or datasets. -### Analyze RNAseq data in Data Studios +### Analyze RNAseq data in Studios -In the **Data Studios** tab, you can monitor and see the details of the data studios in the Community Showcase workspace. +In the **Studios** tab, you can monitor and see the details of the Studios in the Community Showcase workspace. -Data Studios is used to perform bespoke analysis on the results of upstream workflows. For example, in the Community Showcase workspace we have run the **nf-core/rnaseq** pipeline to quantify gene expression, followed by **nf-core/differentialabundance** to derive differential expression statistics. The workspace contains a data studio with these results from cloud storage mounted into the studio to perform further analysis. One of these outputs is an RShiny application, which can be deployed for interactive analysis. +Studios is used to perform bespoke analysis on the results of upstream workflows. For example, in the Community Showcase workspace we have run the **nf-core/rnaseq** pipeline to quantify gene expression, followed by **nf-core/differentialabundance** to derive differential expression statistics. The workspace contains a Studio with these results from cloud storage mounted into the Studio to perform further analysis. One of these outputs is an RShiny application, which can be deployed for interactive analysis. -#### Connect to the RNAseq analysis studio +#### Connect to the RNAseq analysis Studio -Select the `rnaseq_to_differentialabundance` data studio. This studio consists of an RStudio environment that uses an existing compute environment available in the showcase workspace. The studio also contains mounted data generated from the nf-core/rnaseq and subsequent nf-core/differentialabundance pipeline runs, directly from AWS S3. +Select the `rnaseq_to_differentialabundance` Studio. This Studio consists of an RStudio environment that uses an existing compute environment available in the showcase workspace. The Studio also contains mounted data generated from the nf-core/rnaseq and subsequent nf-core/differentialabundance pipeline runs, directly from AWS S3. -![RNAseq studio details](assets/rnaseq-diffab-studio-details.gif) +![RNAseq Studio details](assets/rnaseq-diffab-studio-details.gif) -Select **Connect** to view the running RStudio environment. The `rnaseq_to_differentialabundance` studio includes the necessary R packages for deploying an RShiny application to visualize the RNAseq data. +Select **Connect** to view the running RStudio environment. The `rnaseq_to_differentialabundance` Studio includes the necessary R packages for deploying an RShiny application to visualize the RNAseq data. -Deploy the RShiny app in the data studio by selecting the green play button on the last chunk of the R script: +Deploy the RShiny app in the Studio by selecting the green play button on the last chunk of the R script: ![Run RShiny app](./assets/rnaseq-diffab-run-rshiny-app.png) :::note -Data Studios allows you to specify the resources each studio will use. When [creating your own data studios](../../data_studios/index.mdx) with shared compute environment resources, you must allocate sufficient resources to the compute environment to prevent data studio or pipeline run interruptions. +Studios allows you to specify the resources each Studio will use. When [creating your own Studios](../../studios/index.mdx) with shared compute environment resources, you must allocate sufficient resources to the compute environment to prevent Studio or pipeline run interruptions. ::: ### Explore results @@ -305,12 +305,12 @@ The RShiny app will deploy in a separate browser window, providing a data interf -### Collaborate in the data studio +### Collaborate in the Studio -To share the results of your RNAseq analysis or allow colleagues to perform exploratory analysis, share a link to the data studio by selecting the options menu for the data studio you want to share, then select **Copy data studio URL**. With this link, other authenticated users with the **Connect** [role](../../orgs-and-teams/roles.mdx) (or greater) can access the session directly. +To share the results of your RNAseq analysis or allow colleagues to perform exploratory analysis, share a link to the Studio by selecting the options menu for the Studio you want to share, then select **Copy Studio URL**. With this link, other authenticated users with the **Connect** [role](../../orgs-and-teams/roles.mdx) (or greater) can access the session directly. :::note -See [Data Studios](../../data_studios/index.mdx) to learn how to create data studios in your own workspace. +See [Studios](../../studios/index.mdx) to learn how to create Studios in your own workspace. ::: ## Pipeline optimization diff --git a/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/data-studios.mdx b/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/studios.mdx similarity index 55% rename from platform_versioned_docs/version-24.3/getting-started/quickstart-demo/data-studios.mdx rename to platform_versioned_docs/version-24.3/getting-started/quickstart-demo/studios.mdx index 3cafbcc3d..31f7b6b97 100644 --- a/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/data-studios.mdx +++ b/platform_versioned_docs/version-24.3/getting-started/quickstart-demo/studios.mdx @@ -1,49 +1,49 @@ --- -title: "Data Studios" -description: "An introduction to Data Studios in Seqera Platform" +title: "Studios" +description: "An introduction to Studios in Seqera Platform" date: "8 Jul 2024" -tags: [platform, data, data studios] +tags: [platform, data, studios] --- import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; :::info -This guide provides an introduction to Data Studios using a demo studio in the Community Showcase workspace. See [Data Studios](../../data_studios/index.mdx) to learn how to create data studios in your own workspace. +This guide provides an introduction to Studios using a demo Studio in the Community Showcase workspace. See [Studios](../../studios/index.mdx) to learn how to create Studios in your own workspace. ::: Interactive analysis of pipeline results is often performed in platforms like Jupyter Notebook or RStudio. Setting up the infrastructure for these platforms, including accessing pipeline data and the necessary bioinformatics packages, can be complex and time-consuming. -Data Studios streamlines the process of creating interactive analysis environments for Platform users. With built-in templates, creating a data studio is as simple as adding and sharing pipelines or datasets. Platform manages all the details, enabling you to easily select your preferred interactive tool and analyze your data. +Studios streamlines the process of creating interactive analysis environments for Platform users. With built-in templates, creating a Studio is as simple as adding and sharing pipelines or datasets. Platform manages all the details, enabling you to easily select your preferred interactive tool and analyze your data. -In the **Data Studios** tab, you can monitor and see the details of the data studios in the Community Showcase workspace. +In the **Studios** tab, you can monitor and see the details of the Studios in the Community Showcase workspace. -![Data studios overview](./assets/data-studios-overview.png) +![Studios overview](./assets/studios-overview.png) -Select the options menu next to a data studio to: -- See data studio details -- Start or stop the studio, and connect to a running studio -- Copy the studio URL to share it with collaborators +Select the options menu next to a Studio to: +- See Studio details +- Start or stop the Studio, and connect to a running Studio +- Copy the Studio URL to share it with collaborators -### Analyze RNAseq data in Data Studios +### Analyze RNAseq data in Studios -Data Studios is used to perform bespoke analysis on the results of upstream workflows. For example, in the Community Showcase workspace we have run the nf-core/rnaseq workflow to quantify gene expression, followed by nf-core/differentialabundance to derive differential expression statistics. The workspace contains a data studio with these results from cloud storage mounted into the studio to perform further analysis. One of these outputs is an RShiny application, which can be deployed for interactive analysis. +Studios is used to perform bespoke analysis on the results of upstream workflows. For example, in the Community Showcase workspace we have run the nf-core/rnaseq workflow to quantify gene expression, followed by nf-core/differentialabundance to derive differential expression statistics. The workspace contains a Studio with these results from cloud storage mounted into the Studio to perform further analysis. One of these outputs is an RShiny application, which can be deployed for interactive analysis. -### Open the RNAseq analysis studio +### Open the RNAseq analysis Studio -Select the `rnaseq_to_differentialabundance` data studio. This studio consists of an RStudio environment that uses an existing compute environment available in the showcase workspace. The studio also contains mounted data generated from the nf-core/rnaseq and subsequent nf-core/differentialabundance pipeline runs, directly from AWS S3. +Select the `rnaseq_to_differentialabundance` Studio. This Studio consists of an RStudio environment that uses an existing compute environment available in the showcase workspace. The Studio also contains mounted data generated from the nf-core/rnaseq and subsequent nf-core/differentialabundance pipeline runs, directly from AWS S3. -![RNAseq studio details](assets/rnaseq-diffab-studio-details.gif) +![RNAseq Studio details](assets/rnaseq-diffab-studio-details.gif) :::info -Data Studios allows you to specify the resources each studio will use. When [creating your own data studios](../../data_studios/index.mdx) with shared compute environment resources, you must allocate sufficient resources to the compute environment to prevent data studio or pipeline run interruptions. +Studios allows you to specify the resources each Studio will use. When [creating your own Studios](../../studios/index.mdx) with shared compute environment resources, you must allocate sufficient resources to the compute environment to prevent Studio or pipeline run interruptions. ::: -### Connect to the data studio +### Connect to the Studio -This data studio will start an RStudio environment which already contains the necessary R packages for deploying an RShiny application to interact with various visualizations of the RNAseq data. The studio also contains an R Markdown document with the commands in place to generate the application. +This Studio will start an RStudio environment which already contains the necessary R packages for deploying an RShiny application to interact with various visualizations of the RNAseq data. The Studio also contains an R Markdown document with the commands in place to generate the application. -Deploy the RShiny app in the data studio by selecting the green play button on the last chunk of the R script: +Deploy the RShiny app in the Studio by selecting the green play button on the last chunk of the R script: ![Run RShiny app](./assets/rnaseq-diffab-run-rshiny-app.png) @@ -91,6 +91,6 @@ Using the volcano plot, you can effectively identify and explore the genes with ![RShiny volcano plot](assets/rnaseq-diffab-rshiny-volcano-plot.gif) -### Collaborate in the data studio +### Collaborate in the Studio -To share the results of your RNAseq analysis or allow colleagues to perform exploratory analysis, share a link to the data studio by selecting the options menu for the data studio you want to share, then select **Copy data studio URL**. With this link, other authenticated users with the **Connect** [role](../../orgs-and-teams/roles.mdx) (or greater) can access the session directly. +To share the results of your RNAseq analysis or allow colleagues to perform exploratory analysis, share a link to the Studio by selecting the options menu for the Studio you want to share, then select **Copy Studio URL**. With this link, other authenticated users with the **Connect** [role](../../orgs-and-teams/roles.mdx) (or greater) can access the session directly. diff --git a/platform_versioned_docs/version-24.3/monitoring/dashboard.mdx b/platform_versioned_docs/version-24.3/monitoring/dashboard.mdx index 2a88bba0a..24cb26524 100644 --- a/platform_versioned_docs/version-24.3/monitoring/dashboard.mdx +++ b/platform_versioned_docs/version-24.3/monitoring/dashboard.mdx @@ -8,7 +8,7 @@ tags: [dashboard, pipeline runs, monitoring] The Seqera Platform **Dashboard** is accessed from the user menu and provides an overview of: - Pipeline runs in your personal and organization workspaces. -- Data studio sessions in your organization workspaces only. +- Studio sessions in your organization workspaces only. ## Pipelines @@ -31,9 +31,9 @@ For a detailed view, you can do one of the following: - Select a pipeline integer value in the table to navigate to a list filtered by the status and time range selected. - Select a workspace name in the table to navigate to a list filtered by the workspace selected. -## Data Studios +## Studios -You can explore the status of data studio sessions in your organizational workspaces. On the **Dashboard** page, select **Data Studios**. The following statuses are listed with the number of data studio sessions in each status: +You can explore the status of Studio sessions in your organizational workspaces. On the **Dashboard** page, select **Studios**. The following statuses are listed with the number of Studio sessions in each status: - `Building` - `Build-failed` @@ -53,4 +53,4 @@ Select **Export data** in the view panel near the top of the page to export a CS -[ds]: ../data_studios/index.mdx +[ds]: ../studios/index.mdx From 657e5c8706c189bfbed1b65976c18ac58db5f7ea Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 18 Feb 2025 00:28:07 +0200 Subject: [PATCH 07/30] Changes --- platform_versioned_docs/version-24.2/cli/commands.mdx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/platform_versioned_docs/version-24.2/cli/commands.mdx b/platform_versioned_docs/version-24.2/cli/commands.mdx index 42a1d91fc..d925bbfe6 100644 --- a/platform_versioned_docs/version-24.2/cli/commands.mdx +++ b/platform_versioned_docs/version-24.2/cli/commands.mdx @@ -272,7 +272,7 @@ https://api.cloud.seqera.io/workspaces/97652229034xxx/datasets/6vBGj6aWWpBuLpGKj Run `tw studios -h` to view the list of supported operations. -Manage [Studio sessions](../data_studios/index.mdx) hosted in Seqera Platform. Studio sessions allow interactive analysis using Jupyter, RStudio, VSCode, and Xpra. Additional custom analysis environments can be defined as needed. +Manage [Studio sessions](../studios/index.mdx) hosted in Seqera Platform. Studio sessions allow interactive analysis using Jupyter, RStudio, VSCode, and Xpra. Additional custom analysis environments can be defined as needed. :::note Most Studio operations require workspace `MAINTAIN` permissions. @@ -329,7 +329,7 @@ Build reports | NA Run `tw studios templates -h` to view the required and optional fields for session templates. -Templates are the container image templates used as the foundation for Studio sessions. See [Container image templates](../data_studios/index.mdx#container-image-templates) for more information. +Templates are the container image templates used as the foundation for Studio sessions. See [Container image templates](../studios/index.mdx#container-image-templates) for more information. ```bash tw studios templates -w community/showcase @@ -391,7 +391,7 @@ tw studios stop -i 13083356 -w community/showcase Run `tw studios checkpoints -h` to view the required and optional fields for viewing checkpoints for a session. -List all checkpoints for an existing Studio session in a workspace. See [Session checkpoints](../data_studios/index.mdx#session-checkpoints) for more information. +List all checkpoints for an existing Studio session in a workspace. See [Session checkpoints](../studios/index.mdx#session-checkpoints) for more information. ```bash tw studios checkpoints -i 19a3abbd -w community/showcase From 93dc6e441a02bf6508da7734ace6bcd1b0797382 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 18 Feb 2025 00:48:04 +0200 Subject: [PATCH 08/30] revert two changes --- platform_versioned_docs/version-24.2/cli/commands.mdx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/platform_versioned_docs/version-24.2/cli/commands.mdx b/platform_versioned_docs/version-24.2/cli/commands.mdx index d925bbfe6..52112af95 100644 --- a/platform_versioned_docs/version-24.2/cli/commands.mdx +++ b/platform_versioned_docs/version-24.2/cli/commands.mdx @@ -272,7 +272,7 @@ https://api.cloud.seqera.io/workspaces/97652229034xxx/datasets/6vBGj6aWWpBuLpGKj Run `tw studios -h` to view the list of supported operations. -Manage [Studio sessions](../studios/index.mdx) hosted in Seqera Platform. Studio sessions allow interactive analysis using Jupyter, RStudio, VSCode, and Xpra. Additional custom analysis environments can be defined as needed. +Manage [Studio sessions](../data_studios/index.mdx) hosted in Seqera Platform. Studio sessions allow interactive analysis using Jupyter, RStudio, VSCode, and Xpra. Additional custom analysis environments can be defined as needed. :::note Most Studio operations require workspace `MAINTAIN` permissions. @@ -391,7 +391,7 @@ tw studios stop -i 13083356 -w community/showcase Run `tw studios checkpoints -h` to view the required and optional fields for viewing checkpoints for a session. -List all checkpoints for an existing Studio session in a workspace. See [Session checkpoints](../studios/index.mdx#session-checkpoints) for more information. +List all checkpoints for an existing Studio session in a workspace. See [Session checkpoints](../data_studios/index.mdx#session-checkpoints) for more information. ```bash tw studios checkpoints -i 19a3abbd -w community/showcase From 87336d197eb074a88d5a5319af8a696ce81d2cfc Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 18 Feb 2025 00:48:53 +0200 Subject: [PATCH 09/30] Two fixes --- platform_versioned_docs/version-24.3/cli/commands.mdx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/platform_versioned_docs/version-24.3/cli/commands.mdx b/platform_versioned_docs/version-24.3/cli/commands.mdx index 02101a162..d925bbfe6 100644 --- a/platform_versioned_docs/version-24.3/cli/commands.mdx +++ b/platform_versioned_docs/version-24.3/cli/commands.mdx @@ -329,7 +329,7 @@ Build reports | NA Run `tw studios templates -h` to view the required and optional fields for session templates. -Templates are the container image templates used as the foundation for Studio sessions. See [Container image templates](../data_studios/index.mdx#container-image-templates) for more information. +Templates are the container image templates used as the foundation for Studio sessions. See [Container image templates](../studios/index.mdx#container-image-templates) for more information. ```bash tw studios templates -w community/showcase @@ -391,7 +391,7 @@ tw studios stop -i 13083356 -w community/showcase Run `tw studios checkpoints -h` to view the required and optional fields for viewing checkpoints for a session. -List all checkpoints for an existing Studio session in a workspace. See [Session checkpoints](../data_studios/index.mdx#session-checkpoints) for more information. +List all checkpoints for an existing Studio session in a workspace. See [Session checkpoints](../studios/index.mdx#session-checkpoints) for more information. ```bash tw studios checkpoints -i 19a3abbd -w community/showcase From 5ae9dd4e631f1630b20eb8e1e150da5046404a08 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 18 Feb 2025 00:58:09 +0200 Subject: [PATCH 10/30] . --- platform_versioned_docs/version-24.2/cli/commands.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_docs/version-24.2/cli/commands.mdx b/platform_versioned_docs/version-24.2/cli/commands.mdx index 52112af95..42a1d91fc 100644 --- a/platform_versioned_docs/version-24.2/cli/commands.mdx +++ b/platform_versioned_docs/version-24.2/cli/commands.mdx @@ -329,7 +329,7 @@ Build reports | NA Run `tw studios templates -h` to view the required and optional fields for session templates. -Templates are the container image templates used as the foundation for Studio sessions. See [Container image templates](../studios/index.mdx#container-image-templates) for more information. +Templates are the container image templates used as the foundation for Studio sessions. See [Container image templates](../data_studios/index.mdx#container-image-templates) for more information. ```bash tw studios templates -w community/showcase From 6fc7c46d4bda5d3dbe4eba92649f103e2fbe57a8 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 18 Feb 2025 08:25:06 +0200 Subject: [PATCH 11/30] Troubleshooting updates --- ...ooting.mdx => studios_troubleshooting.mdx} | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) rename platform_versioned_docs/version-24.3/troubleshooting_and_faqs/{data_studios_troubleshooting.mdx => studios_troubleshooting.mdx} (79%) diff --git a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/data_studios_troubleshooting.mdx b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx similarity index 79% rename from platform_versioned_docs/version-24.3/troubleshooting_and_faqs/data_studios_troubleshooting.mdx rename to platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx index a7d6e9e44..71fe7d290 100644 --- a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/data_studios_troubleshooting.mdx +++ b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx @@ -1,6 +1,6 @@ --- -title: "Data Studios" -description: "Data Studios troubleshooting with Seqera Platform." +title: "Studios" +description: "Studios troubleshooting with Seqera Platform." date: "26 August 2024" tags: [faq, help, data studios, troubleshooting] --- @@ -11,35 +11,35 @@ In your interactive analysis environment, open a new terminal and type `ls -la / ![](./_images/data_studios_notebook_fusion.png) -## Data Studio session is stuck in **starting** +## Studio session is stuck in **starting** If your studio session doesn't advance from **starting** status to **running** status within 30 minutes, and you have access to the AWS Console for your organization, check that the AWS Batch compute environment associated with the data studio session is in the **ENABLED** state with a **VALID** status. You can also check the **Compute resources** settings. Contact your organization's AWS administrator if you don't have access to the AWS Console. If sufficient compute environment resources are unavailable, **Stop** the studio session and any others that may be running before trying again. If you have access to the AWS Console for your organization, you can terminate a specific session from the AWS Batch Jobs page (filtering by compute environment queue). -## Data Studio session status is **errored** +## Studio session status is **errored** The **errored** status is generally related to issues encountered when creating the studio session resources in the compute environment (e.g., invalid credentials, insufficient permissions, network issues). It can also be related to insufficient compute resources, which are set in your compute environment configuration. Contact your organization's AWS administrator if you don't have access to the AWS Console. Also contact your Seqera account executive so we can investigate the issue. -## Data Studio session can't be **stopped** +## Studio session can't be **stopped** -If you're not able to stop a studio session, it's usually because the Batch job running the session failed for some reason. In this case, and if you have access to the AWS Console for your organization, you can stop the session from the compute environment screen. Contact your organization's AWS administrator if you don't have access to the AWS Console. Also contact your Seqera account executive so we can investigate the issue. +If you're not able to stop a session, it's usually because the Batch job running the session failed for some reason. In this case, and if you have access to the AWS Console for your organization, you can stop the session from the compute environment screen. Contact your organization's AWS administrator if you don't have access to the AWS Console. Also contact your Seqera account executive so we can investigate the issue. -## Data Studio session performance is poor +## Studio session performance is poor -A slow or unresponsive studio session may be due to its AWS Batch compute environment being utilized for other jobs, such as running Nextflow pipelines. The compute environment is responsible for scheduling jobs to the available compute resources. Data Studio sessions compete for resources with the Nextflow pipeline head job and Seqera does not currently have an established pattern of precedence. +A slow or unresponsive session may be due to its AWS Batch compute environment being utilized for other jobs, such as running Nextflow pipelines. The compute environment is responsible for scheduling jobs to the available compute resources. Studio sessions compete for resources with the Nextflow pipeline head job and Seqera does not currently have an established pattern of precedence. If you have access to the AWS Console for your organization, check the jobs associated with the AWS Batch compute environment and compare the resources allocated with its **Compute resources** settings. -## Memory allocation of the Data Studio session is exceeded +## Memory allocation of the Studio session is exceeded -The running container in the AWS Batch compute environment inherits the memory limits specified by the studio session configuration when adding or starting the session. The kernel then handles the memory as if running natively on Linux. Linux can overcommit memory, leading to possible out-of-memory errors in a container environment. The kernel has protections in place to prevent this, but it can happen, and in this case, the process is killed. This can manifest as a performance lag, killed subprocesses, or at worst, a killed data studio session. Running studio sessions have automated snapshots created every five minutes, so if the running container is killed only those changes made after the prior snapshot creation will be lost. +The running container in the AWS Batch compute environment inherits the memory limits specified by the studio session configuration when adding or starting the session. The kernel then handles the memory as if running natively on Linux. Linux can overcommit memory, leading to possible out-of-memory errors in a container environment. The kernel has protections in place to prevent this, but it can happen, and in this case, the process is killed. This can manifest as a performance lag, killed subprocesses, or at worst, a killed session. Running sessions have automated snapshots created every five minutes, so if the running container is killed only those changes made after the prior snapshot creation will be lost. ## All datasets are read-only By default, AWS Batch compute environments that are created with Batch Forge restrict access to S3 to the working directory only, unless additional **Allowed S3 Buckets** are specified. If the compute environment does not have write access to the mounted dataset, it will be mounted as read-only. -## My Data Studio session with GPU isn't starting +## My Studio session with GPU isn't starting Check whether the instance type you selected [supports GPU](https://aws.amazon.com/ec2/instance-types/). If you specify multiple GPUs make sure that multi-GPU instances can be launched by your compute environment and are not limited by the maximum CPU config that you've set. From 8f871237203800f9a76406d3432457b9cbde7b28 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 18 Feb 2025 08:31:10 +0200 Subject: [PATCH 12/30] build fix --- platform_versioned_sidebars/version-24.3-sidebars.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_sidebars/version-24.3-sidebars.json b/platform_versioned_sidebars/version-24.3-sidebars.json index 07719e0c5..5d767a0ff 100644 --- a/platform_versioned_sidebars/version-24.3-sidebars.json +++ b/platform_versioned_sidebars/version-24.3-sidebars.json @@ -207,7 +207,7 @@ "items": [ "troubleshooting_and_faqs/troubleshooting", "troubleshooting_and_faqs/api_and_cli", - "troubleshooting_and_faqs/data_studios_troubleshooting", + "troubleshooting_and_faqs/studios_troubleshooting", "troubleshooting_and_faqs/nextflow", "troubleshooting_and_faqs/aws_troubleshooting", "troubleshooting_and_faqs/azure_troubleshooting", From 6ffafea6c1ab847c515c441e4c96e93847432892 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 00:01:29 +0200 Subject: [PATCH 13/30] Updated enterprise deployment docs --- .../{data-studios.mdx => studios.mdx} | 40 +++++++++---------- .../version-24.2-sidebars.json | 2 +- 2 files changed, 21 insertions(+), 21 deletions(-) rename platform_versioned_docs/version-24.2/enterprise/{data-studios.mdx => studios.mdx} (82%) diff --git a/platform_versioned_docs/version-24.2/enterprise/data-studios.mdx b/platform_versioned_docs/version-24.2/enterprise/studios.mdx similarity index 82% rename from platform_versioned_docs/version-24.2/enterprise/data-studios.mdx rename to platform_versioned_docs/version-24.2/enterprise/studios.mdx index dbf176564..8f64a8ce0 100644 --- a/platform_versioned_docs/version-24.2/enterprise/data-studios.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/studios.mdx @@ -1,11 +1,11 @@ --- -title: "Data Studios deployment" +title: "Studios deployment" description: Deploy Seqera Platform with Data studios date: "12 Jun 2024" tags: [docker, compose, kubernetes, data, studios, deployment] --- -Enable Data Studios as part of your Seqera Platform instance. You must have Data Explorer enabled to use Data Studios. Only the Amazon AWS public cloud is currently supported. +Enable Studios as part of your Seqera Platform instance. You must have Data Explorer enabled to use Data Studios. Only the Amazon AWS public cloud is currently supported. :::caution You must complete the upgrade of your Platform Enterprise installation to version 24.1.4 before enabling and configuring Data Studios. @@ -13,27 +13,27 @@ You must complete the upgrade of your Platform Enterprise installation to versio ## DNS configuration -Each data studio is reachable at a unique URL that includes a randomly generated subdomain name. For example: `https://abcd.example.com/`, where `example.com` is your Seqera base domain name. +Each Studio is reachable at a unique URL that includes a randomly generated subdomain name. For example: `https://abcd.example.com/`, where `example.com` is your Seqera base domain name. Provide a wildcard TLS certificate to allow for uniquely generated subdomains. A wildcard certificate common name includes `*.` in the domain name, such as `*.example.com`, thereby securing any subdomain name at this level. -Data Studios uses the following set of domains and subdomains: +Studios uses the following set of domains and subdomains: - The domain that you set for `TOWER_SERVER_URL`, such as `example.com`. - A wildcard subdomain that you must configure specifically for Data Studios. This wildcard subdomain is the parent for each unique data studios session URL, such as `abcd.example.com`. - The connection proxy, defined by `CONNECT_PROXY_URL`. This URL is a first-level subdomain of your `TOWER_SERVER_URL`. For example, `https://connect.example.com`. -## Data Studios workspace availability +## Studios workspace availability -You can configure which organizational workspaces have access to Data Studios. This configuration is set in the `tower.yml` file. The `tower.data-studio.allowed-workspaces` field supports the following options: +You can configure which organizational workspaces have access to Studios. This configuration is set in the `tower.yml` file. The `tower.data-studio.allowed-workspaces` field supports the following options: -- `allowed-workspaces: []`: Disables Data Studios. This is the default if the `allowed-workspaces` field is not specified. -- `allowed-workspaces: [ , ]`: Enables Data Studios for the comma-separated list of organizational workspace IDs. -- `allowed-workspaces: null`: Enables Data Studios for all organizational workspaces. +- `allowed-workspaces: []`: Disables Studios. This is the default if the `allowed-workspaces` field is not specified. +- `allowed-workspaces: [ , ]`: Enables Studios for the comma-separated list of organizational workspace IDs. +- `allowed-workspaces: null`: Enables Studios for all organizational workspaces. ## Available data studio environment images -Each of the provided Data Studios environments includes a particular version of the underlying data analytics software package. +Each of the provided Studios environments includes a particular version of the underlying data analytics software package. To quickly identify which version of the software an image includes, the version string for each container is in the form of `-`. For example, if the version string for the RStudio Server is `4.4.1-0.7.4`, version `4.4.1` is the RStudio version and `0.7.4` is the version of this Seqera-built container image. @@ -93,11 +93,11 @@ This guide assumes that all services will be run in the same container as the re 1. Open `tower.env` in an editor and set the following variables: - `TOWER_DATA_EXPLORER_ENABLED`: Set `true` to enable Data Explorer. You must enable Data Explorer to mount data inside a data studio instance. - - `TOWER_DATA_STUDIO_CONNECT_URL`: The URL of the Data Studios connect proxy, such as `https://connect.example.com/`. + - `TOWER_DATA_STUDIO_CONNECT_URL`: The URL of the Studios connect proxy, such as `https://connect.example.com/`. - `TOWER_OIDC_REGISTRATION_INITIAL_ACCESS_TOKEN`: The same value set in the `oidc_registration_token` environment variable. - `TOWER_OIDC_PEM_PATH`: The file path to a PEM certificate used for signing the OIDC tokens for the OpenID connect provider, mounted as a volume inside the container. -1. Edit the `tower.yml` file and include the following snippet to enable Data Studios in all organization workspaces: +1. Edit the `tower.yml` file and include the following snippet to enable Studios in all organization workspaces: ```yaml tower: @@ -113,7 +113,7 @@ This guide assumes that all services will be run in the same container as the re docker ps ``` -1. To confirm that Data Studios is available, log in to your Platform instance and navigate to an organizational workspace that has Data Studios enabled. The **Data Studios** tab is included with the available tabs. +1. To confirm that Studios is available, log in to your Platform instance and navigate to an organizational workspace that has Data Studios enabled. The **Studios** tab is included with the available tabs. ## Kubernetes @@ -121,7 +121,7 @@ This procedure describes how to configure Data Studios for Kubernetes deployment ### Procedure -1. Download the Kubernetes manifests for the Data Studios service: +1. Download the Kubernetes manifests for the Studios service: - [Proxy](./_templates/k8s/data_studios/proxy.yml) - [Server](./_templates/k8s/data_studios/server.yml) @@ -174,7 +174,7 @@ This procedure describes how to configure Data Studios for Kubernetes deployment base64_pem=$(cat data-studios-rsa.pem | base64) ``` -1. Create a Secret file named `secret.yml` and set the `oidc.pem` key by pasting the contents of the base64-encoded public/private key pair: +1. Create a secret file named `secret.yml` and set the `oidc.pem` key by pasting the contents of the base64-encoded public/private key pair: ```yaml apiVersion: v1 @@ -186,17 +186,17 @@ This procedure describes how to configure Data Studios for Kubernetes deployment oidc.pem: ``` -1. Create the Secret: +1. Create the secret: ``` kubectl apply -f secret.yml ``` -1. Edit the `tower-svc.yml` file and uncomment the `volumes.cert-volume`, `volumeMounts.cert-volume`, and `env.TOWER_OIDC_PEM_PATH` fields so that the public/private key pair is available to Platform. +1. Edit the `tower-src.yml` file and uncomment the `volumes.cert-volume`, `volumeMounts.cert-volume`, and `env.TOWER_OIDC_PEM_PATH` fields so that the public/private key pair is available to Platform. 1. Edit the ConfigMap named `platform-backend-cfg` in the `configmap.yml` for Platform by editing the following environment variables: - - `TOWER_DATA_STUDIO_CONNECT_URL`: The URL of the Data Studios connect proxy, such as `https://connect.example.com/`. + - `TOWER_DATA_STUDIO_CONNECT_URL`: The URL of the Studios connect proxy, such as `https://connect.example.com/`. - `TOWER_OIDC_REGISTRATION_INITIAL_ACCESS_TOKEN`: The same value as the `oidc_registration_token` value created previously. 1. Edit the ConfigMap named `tower-yml` in the `configmap.yml` and include the following snippet: @@ -236,7 +236,7 @@ This procedure describes how to configure Data Studios for Kubernetes deployment kubectl scale --replicas=1 deployment/backend ``` -1. Apply the Data Studios manifests: +1. Apply the Studios manifests: ``` kubectl apply -f ingress.aks.yml proxy.yml server.yml @@ -244,4 +244,4 @@ This procedure describes how to configure Data Studios for Kubernetes deployment It can take several minutes for Kubernetes to apply your changes, during which new pods are rolled out. -1. To confirm that Data Studios is available, log in to your Platform instance and navigate to an organizational workspace that has Data Studios enabled. The **Data Studios** tab is included with the available tabs. +1. To confirm that Studios is available, log in to your Platform instance and navigate to an organizational workspace that has Studios enabled. The **Studios** tab is included with the available tabs. diff --git a/platform_versioned_sidebars/version-24.2-sidebars.json b/platform_versioned_sidebars/version-24.2-sidebars.json index daa6a1182..11d35746f 100644 --- a/platform_versioned_sidebars/version-24.2-sidebars.json +++ b/platform_versioned_sidebars/version-24.2-sidebars.json @@ -165,7 +165,7 @@ "enterprise/configuration/ssl_tls", "enterprise/configuration/pipeline_optimization", "enterprise/configuration/wave", - "enterprise/data-studios" + "enterprise/studios" ] }, { From 6d20aaf7926913365fcbe5611d844ca6656c21ae Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 17:06:44 +0200 Subject: [PATCH 14/30] Fixing broken internal links. --- .../version-24.2/enterprise/docker-compose.mdx | 8 ++++---- .../version-24.2/enterprise/kubernetes.mdx | 10 +++++----- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx b/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx index f7423ac7d..4f6d4b59b 100644 --- a/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx @@ -25,7 +25,7 @@ The DB or Redis volume is persistent after a Docker restart by default. Use the - To configure the Seqera pipeline resource optimization service (`groundswell`), see [Pipeline resource optimization](./configuration/pipeline_optimization.mdx). - - To deploy with Data Studios, see [Data studios deployment](../enterprise/data-studios.mdx). + - To deploy with Studios, see [Data studios deployment](../enterprise/studios.mdx). 4. Deploy the application and wait for it to initialize (this process takes a few minutes): @@ -43,10 +43,10 @@ For more information on configuration, see [Configuration options](./configurati ## Optional features -### Data Studios +### Studios -[Data Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Data Studios, see [Data Studios deployment](./data-studios.mdx). +[Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](./studios.mdx). :::note -Data Studios is currently in **public preview** and is available from Seqera Platform v24.1. If you experience any problems during the deployment process please contact your account executive. Data Studios in Enterprise is not installed by default. +Studios is currently in **public preview** and is available from Seqera Platform v24.1. If you experience any problems during the deployment process please contact your account executive. Data Studios in Enterprise is not installed by default. ::: diff --git a/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx b/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx index c0ccf6149..5d8fbf3fe 100644 --- a/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx @@ -43,8 +43,8 @@ Seqera Enterprise is distributed as a collection of Docker containers available ```bash kubectl create secret docker-registry cr.seqera.io \ --docker-server=cr.seqera.io \ - --docker-username='' \ - --docker-password='' + --docker-username='' \ + --docker-password='' ``` The credential `name` contains a dollar `$` character. Wrap the name in single quotes to prevent the Linux shell from interpreting this value as an environment variable. @@ -250,12 +250,12 @@ Define a set of credentials for the resource optimization database in the `tower The initContainers will wait until both the Seqera and pipeline optimization service databases are ready before starting the migration in the Seqera database and finally starting the resource optimization container. -### Data Studios +### Studios -[Data Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Data Studios, see [Data Studios deployment](./data-studios.mdx). +[Data Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Data Studios, see [Studios deployment](./studios.mdx). :::note -Data Studios is currently in **public preview** and is available from Seqera Platform v24.1. If you experience any problems during the deployment process [contact Seqera support](https://support.seqera.io). Data Studios in Enterprise is not installed by default. +Studios is currently in **public preview** and is available from Seqera Platform v24.1. If you experience any problems during the deployment process [contact Seqera support](https://support.seqera.io). Studios in Enterprise is not installed by default. ::: ### Database console From 0dbcae79ebd51568a25ccc2a41046a1970c9b960 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 17:16:42 +0200 Subject: [PATCH 15/30] Fixed broken internal links --- platform_versioned_docs/version-24.2/data_studios/index.mdx | 2 +- platform_versioned_docs/version-24.3/studios/index.mdx | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/platform_versioned_docs/version-24.2/data_studios/index.mdx b/platform_versioned_docs/version-24.2/data_studios/index.mdx index 05258cd0e..5baa6c776 100644 --- a/platform_versioned_docs/version-24.2/data_studios/index.mdx +++ b/platform_versioned_docs/version-24.2/data_studios/index.mdx @@ -10,7 +10,7 @@ Studios is a unified platform where you can host a combination of container imag On Seqera Cloud, the free tier permits only one running session at a time. To run simultaneous sessions, [contact Seqera][contact] for a Seqera Cloud Pro license. :::note -Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Studios in Enterprise is not enabled by default. You can enable it in the [environment variables configuration](../enterprise/data-studios.mdx). +Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Studios in Enterprise is not enabled by default. You can enable it in the [environment variables configuration](../enterprise/studios.mdx). ::: ## Requirements diff --git a/platform_versioned_docs/version-24.3/studios/index.mdx b/platform_versioned_docs/version-24.3/studios/index.mdx index fd0c4d278..cba0bfcb3 100644 --- a/platform_versioned_docs/version-24.3/studios/index.mdx +++ b/platform_versioned_docs/version-24.3/studios/index.mdx @@ -10,7 +10,7 @@ Studios is a unified platform where you can host a combination of container imag On Seqera Cloud, the free tier permits only one running session at a time. To run simultaneous sessions, [contact Seqera][contact] for a Seqera Cloud Pro license. :::note -Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Data Studios in Enterprise is not enabled by default. You can enable Data Studios in the [environment variables configuration](../../version-24.2/enterprise/data-studios.mdx). +Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Data Studios in Enterprise is not enabled by default. You can enable Data Studios in the [environment variables configuration](../../version-24.2/enterprise/studios.mdx). ::: ## Requirements From e1eca089581a7c17998f3af98e8ed16702f21dbc Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 17:25:45 +0200 Subject: [PATCH 16/30] broken internal link --- ...ebook_fusion.png => studios_notebook_fusion.png} | Bin .../studios_troubleshooting.mdx | 4 ++-- 2 files changed, 2 insertions(+), 2 deletions(-) rename platform_versioned_docs/version-24.3/troubleshooting_and_faqs/_images/{data_studios_notebook_fusion.png => studios_notebook_fusion.png} (100%) diff --git a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/_images/data_studios_notebook_fusion.png b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/_images/studios_notebook_fusion.png similarity index 100% rename from platform_versioned_docs/version-24.3/troubleshooting_and_faqs/_images/data_studios_notebook_fusion.png rename to platform_versioned_docs/version-24.3/troubleshooting_and_faqs/_images/studios_notebook_fusion.png diff --git a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx index 71fe7d290..eeb2091a5 100644 --- a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx +++ b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx @@ -9,7 +9,7 @@ tags: [faq, help, data studios, troubleshooting] In your interactive analysis environment, open a new terminal and type `ls -la /workspace/data`. This displays all the mounted datasets available in the current studio session. -![](./_images/data_studios_notebook_fusion.png) +![](./_images/studios_notebook_fusion.png) ## Studio session is stuck in **starting** @@ -58,7 +58,7 @@ This is displayed because logging is set to `stderr` by default to ensure all lo ### VSCode -When running an SCA security scan (e.g., with Trivy) on the latest Seqera-provided VSCode image [container template](../data_studios#container-image-templates), you may encounter multiple false-positive findings. This issue is due to how VSCode defines extensions, which can cause certain security scanners to incorrectly identify them as `npm` packages. +When running an SCA security scan (e.g., with Trivy) on the latest Seqera-provided VSCode image [container template](../studios#container-image-templates), you may encounter multiple false-positive findings. This issue is due to how VSCode defines extensions, which can cause certain security scanners to incorrectly identify them as `npm` packages. This is a known limitation and has been discussed in the Trivy community [here(https://github.com/aquasecurity/trivy/discussions/6112)]. From c0038cc6eadf2929db58f1a385a2dde090d83a5d Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 17:37:01 +0200 Subject: [PATCH 17/30] Fixed homepage links --- src/modules/Homepage/index.tsx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/modules/Homepage/index.tsx b/src/modules/Homepage/index.tsx index 30c2e6bf2..21edc0840 100644 --- a/src/modules/Homepage/index.tsx +++ b/src/modules/Homepage/index.tsx @@ -158,10 +158,10 @@ export default function Home(): JSX.Element {
-

Data Studios

+

Studios

    -
  • Data Studios overview
    • -
  • Deploy Data Studios
    • +
  • Studios overview
    • +
  • Studios
  • Data Explorer
From 45102355659a983d3de08f7c0f61fb5110468eeb Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 17:44:51 +0200 Subject: [PATCH 18/30] Additional naming changes and fixes --- .../version-24.2/enterprise/studios.mdx | 14 +++++++------- .../version-24.3/studios/custom-envs.mdx | 12 ++++++------ .../version-24.3/studios/index.mdx | 4 ++-- .../version-24.3/studios/managing.mdx | 14 +++++++------- .../studios_troubleshooting.mdx | 2 +- 5 files changed, 23 insertions(+), 23 deletions(-) diff --git a/platform_versioned_docs/version-24.2/enterprise/studios.mdx b/platform_versioned_docs/version-24.2/enterprise/studios.mdx index 8f64a8ce0..41a612fa2 100644 --- a/platform_versioned_docs/version-24.2/enterprise/studios.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/studios.mdx @@ -20,7 +20,7 @@ Provide a wildcard TLS certificate to allow for uniquely generated subdomains. A Studios uses the following set of domains and subdomains: - The domain that you set for `TOWER_SERVER_URL`, such as `example.com`. -- A wildcard subdomain that you must configure specifically for Data Studios. This wildcard subdomain is the parent for each unique data studios session URL, such as `abcd.example.com`. +- A wildcard subdomain that you must configure specifically for Studios. This wildcard subdomain is the parent for each unique Studios session URL, such as `abcd.example.com`. - The connection proxy, defined by `CONNECT_PROXY_URL`. This URL is a first-level subdomain of your `TOWER_SERVER_URL`. For example, `https://connect.example.com`. ## Studios workspace availability @@ -31,7 +31,7 @@ You can configure which organizational workspaces have access to Studios. This c - `allowed-workspaces: [ , ]`: Enables Studios for the comma-separated list of organizational workspace IDs. - `allowed-workspaces: null`: Enables Studios for all organizational workspaces. -## Available data studio environment images +## Available Studio environment images Each of the provided Studios environments includes a particular version of the underlying data analytics software package. @@ -56,7 +56,7 @@ This guide assumes that all services will be run in the same container as the re ### Procedure -1. Download the Data Studios [environment configuration file](./_templates/docker/data-studios.env). +1. Download the Studios [environment configuration file](./_templates/docker/data-studios.env). 1. Create an initial OIDC registration token, which can be any secure random string. For example, using openssl: @@ -92,7 +92,7 @@ This guide assumes that all services will be run in the same container as the re 1. Open `tower.env` in an editor and set the following variables: - - `TOWER_DATA_EXPLORER_ENABLED`: Set `true` to enable Data Explorer. You must enable Data Explorer to mount data inside a data studio instance. + - `TOWER_DATA_EXPLORER_ENABLED`: Set `true` to enable Data Explorer. You must enable Data Explorer to mount data inside a Studio. - `TOWER_DATA_STUDIO_CONNECT_URL`: The URL of the Studios connect proxy, such as `https://connect.example.com/`. - `TOWER_OIDC_REGISTRATION_INITIAL_ACCESS_TOKEN`: The same value set in the `oidc_registration_token` environment variable. - `TOWER_OIDC_PEM_PATH`: The file path to a PEM certificate used for signing the OIDC tokens for the OpenID connect provider, mounted as a volume inside the container. @@ -113,11 +113,11 @@ This guide assumes that all services will be run in the same container as the re docker ps ``` -1. To confirm that Studios is available, log in to your Platform instance and navigate to an organizational workspace that has Data Studios enabled. The **Studios** tab is included with the available tabs. +1. To confirm that Studios is available, log in to your Platform instance and navigate to an organizational workspace that has Studios enabled. The **Studios** tab is included with the available tabs. ## Kubernetes -This procedure describes how to configure Data Studios for Kubernetes deployments of Seqera Platform. +This procedure describes how to configure Studios for Kubernetes deployments of Seqera Platform. ### Procedure @@ -143,7 +143,7 @@ This procedure describes how to configure Data Studios for Kubernetes deployment 1. Edit the `proxy.yml` file and set the following variables: - `CONNECT_REDIS_ADDRESS`: The hostname or IP address of the Redis server configured for Platform. - - `CONNECT_PROXY_URL`: A URL for the connect proxy subdomain. We recommend you set a first-level subdomain of your Platform installation domain (`PLATFORM_URL` below) for your connect proxy, to be able to use the same wildcard TLS certificate for all data studio instance URLs and avoid additional domain nesting. For example, `https://connect.example.com`. + - `CONNECT_PROXY_URL`: A URL for the connect proxy subdomain. We recommend you set a first-level subdomain of your Platform installation domain (`PLATFORM_URL` below) for your connect proxy, to be able to use the same wildcard TLS certificate for all Studio session URLs and avoid additional domain nesting. For example, `https://connect.example.com`. - `PLATFORM_URL`: The base URL for your Platform installation, such as `https://example.com/`. - `CONNECT_OIDC_CLIENT_REGISTRATION_TOKEN`: The same value as the `oidc_registration_token` value created previously. diff --git a/platform_versioned_docs/version-24.3/studios/custom-envs.mdx b/platform_versioned_docs/version-24.3/studios/custom-envs.mdx index a657b0b70..900e39266 100644 --- a/platform_versioned_docs/version-24.3/studios/custom-envs.mdx +++ b/platform_versioned_docs/version-24.3/studios/custom-envs.mdx @@ -2,7 +2,7 @@ title: "Custom environments" description: "Custom environments for Studios" date: "1 Oct 2024" -tags: [data, studios] +tags: [environments, custom, studios] --- In addition to the Seqera-provided container template images, you can provide your own custom container environments by augmenting the Seqera-provided images with a list of Conda packages or by providing your own base container template image. @@ -33,7 +33,7 @@ dependencies: - seaborn ``` -To create a data studio with custom Conda packages, see [Add a data studio][add-ds]. +To create a Studio with custom Conda packages, see [Add a Studio][add-s]. ## Custom container template image {#custom-containers} @@ -50,9 +50,9 @@ Public container registries are supported by default. Amazon Elastic Container R ### Dockerfile configuration {#dockerfile} -For your custom template container image, you must use a Seqera-provided base image and include several additional build steps for compatibility with Data Studios. +For your custom template container image, you must use a Seqera-provided base image and include several additional build steps for compatibility with Studios. -To create a data studio with a custom template image, see [Add a data studio][add-ds]. +To create a Studio with a custom template image, see [Add a Studio][add-s]. #### Ports @@ -86,7 +86,7 @@ RUN /usr/bin/connect-client --install ENTRYPOINT ["/usr/bin/connect-client", "--entrypoint"] ``` -For example, to run a basic Python-based HTTP server, build a container from the following Dockerfile. When a data studio runs the custom template environment, the value for the `CONNECT_TOOL_PORT` environment variable is provided dynamically. +For example, to run a basic Python-based HTTP server, build a container from the following Dockerfile. When a Studio runs the custom template environment, the value for the `CONNECT_TOOL_PORT` environment variable is provided dynamically. ```docker title="Example Dockerfile with Python HTTP server" FROM public.cr.seqera.io/platform/connect-client:0.7 AS connect @@ -105,7 +105,7 @@ CMD ["/usr/bin/bash", "-c", "python3 -m http.server $CONNECT_TOOL_PORT"] You can inspect the progress of a custom container template image build, including any errors if the build fails. A link to the [Wave service][wave-home] container build report is always available for builds. -If the custom container template image build fails, the data studio session has the **build-failed** status. The details about build failures are available when inspecting the session details in the **Error report** tab. +If the custom container template image build fails, the Studio session has the **build-failed** status. The details about build failures are available when inspecting the session details in the **Error report** tab. To inspect the status of an ongoing build, or a successful or failed build, complete the following steps: diff --git a/platform_versioned_docs/version-24.3/studios/index.mdx b/platform_versioned_docs/version-24.3/studios/index.mdx index cba0bfcb3..64b3ad525 100644 --- a/platform_versioned_docs/version-24.3/studios/index.mdx +++ b/platform_versioned_docs/version-24.3/studios/index.mdx @@ -10,7 +10,7 @@ Studios is a unified platform where you can host a combination of container imag On Seqera Cloud, the free tier permits only one running session at a time. To run simultaneous sessions, [contact Seqera][contact] for a Seqera Cloud Pro license. :::note -Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Data Studios in Enterprise is not enabled by default. You can enable Data Studios in the [environment variables configuration](../../version-24.2/enterprise/studios.mdx). +Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Studios in Enterprise is not enabled by default. You can enable Studios in the [environment variables configuration](../../version-24.2/enterprise/studios.mdx). ::: ## Requirements @@ -150,7 +150,7 @@ When you stop and start a Studio session, or start a new Studio session from a p Checkpoints can be renamed and the name has to be unique per Studio. Spaces in checkpoint names are converted to underscores automatically. -Checkpoint files in the compute environment work directory may be shared by multiple data studios. Each checkpoint file is cleaned up asynchronously after the last Studio referencing the checkpoint is deleted. +Checkpoint files in the compute environment work directory may be shared by multiple Studios. Each checkpoint file is cleaned up asynchronously after the last Studio referencing the checkpoint is deleted. :::note The cleanup process is a best effort and not guaranteed. Seqera attempts to remove the checkpoint, but it can fail if, for example, the compute environment credentials used do not have sufficient permissions to delete objects from storage buckets. diff --git a/platform_versioned_docs/version-24.3/studios/managing.mdx b/platform_versioned_docs/version-24.3/studios/managing.mdx index 58abb0cf2..9e2fb2f37 100644 --- a/platform_versioned_docs/version-24.3/studios/managing.mdx +++ b/platform_versioned_docs/version-24.3/studios/managing.mdx @@ -2,7 +2,7 @@ title: "Manage Studio sessions" description: "Manage Studio sessions." date: "6 February 2025" -tags: [data, studios] +tags: [data, session, studios] --- Select the **Studios** tab in Platform to view all Studio sessions. The list includes the name, cloud provider, analysis template, region, author, creation date, and status of each session. In this view, you can add a new Studio and start, stop, or connect to an existing session. Dynamically filter the list of Studios using the search bar to search by name (default), author username, or compute environment name. Select a Studio to open a detailed view that displays configuration information. @@ -24,7 +24,7 @@ To add a new Studio, complete the following steps: 1. Select **Mount data**, and then from the **Mount data** modal, select data to mount. Select **Mount data** to confirm your selection. :::tip - Datasets are mounted using the [Fusion file system](https://docs.seqera.io/fusion) and are available at `/workspace/data/`. Mounted data doesn't need to match the compute environment or region of the cloud provider of the data studio. However, this might cause increased costs or errors. + Datasets are mounted using the [Fusion file system](https://docs.seqera.io/fusion) and are available at `/workspace/data/`. Mounted data doesn't need to match the compute environment or region of the cloud provider of the Studio. However, this might cause increased costs or errors. ::: 1. Select **Next**. @@ -34,10 +34,10 @@ To add a new Studio, complete the following steps: - To use one of the Seqera-provided container templates, complete the following steps: 1. Customize the following fields: - - **Container template**: Select a data studio template from the dropdown list. + - **Container template**: Select a Studio template from the dropdown list. - **Studio name** - Optional: **Description** - 1. Optional: Select **Install Conda packages** to enter or upload a list of Conda packages to include with the data studio. For more information on the syntax for specifying Conda packages, see [Conda package syntax][conda-syntax]. + 1. Optional: Select **Install Conda packages** to enter or upload a list of Conda packages to include with the Studio. For more information on the syntax for specifying Conda packages, see [Conda package syntax][conda-syntax]. 1. Select **Next**. - To use a custom container template image that you supply, complete the following steps: @@ -49,7 +49,7 @@ To add a new Studio, complete the following steps: If you select the **Prebuilt container image** template, you cannot select **Install Conda packages** as these options are mutually exclusive. ::: - - **Data studio name** + - **Studio name** - Optional: **Description** 1. Select **Next**. @@ -81,7 +81,7 @@ Once a session is in a **running** state, you can connect to it, obtain the publ This functionality is available to users with the **Maintain** role and above. -You can use any existing Studio as the foundation for adding a new data studio. This functionality creates a clone of the Studio, including its checkpoint history, preserving any modifications made to the original Studio. When you create a session in this way, future changes are isolated from the original session. +You can use any existing Studio as the foundation for adding a new Studio. This functionality creates a clone of the Studio, including its checkpoint history, preserving any modifications made to the original Studio. When you create a session in this way, future changes are isolated from the original session. When adding a new session from an existing session or checkpoint, the following fields cannot be changed: @@ -104,7 +104,7 @@ To connect to a running session, select the three dots next to the status messag An active connection to a session will not prevent administrative actions that might disrupt that connection. For example, a session can be stopped by another workspace user while you are active in the session, the underlying credentials can be changed, or the compute environment can be deleted. These are independent actions and the user in the session won't be alerted to any changes - the only alert will be a server connection error in the active session browser tab. ::: -Once connected, the session will display the status of **running** in the list, and any connected user's avatar will be displayed under the status in both the list of data studios and in each Studio's detail page. +Once connected, the session will display the status of **running** in the list, and any connected user's avatar will be displayed under the status in both the list of Studios and in each Studio's detail page. ## Collaborate in a Studio diff --git a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx index eeb2091a5..3cf6d441e 100644 --- a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx +++ b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx @@ -13,7 +13,7 @@ In your interactive analysis environment, open a new terminal and type `ls -la / ## Studio session is stuck in **starting** -If your studio session doesn't advance from **starting** status to **running** status within 30 minutes, and you have access to the AWS Console for your organization, check that the AWS Batch compute environment associated with the data studio session is in the **ENABLED** state with a **VALID** status. You can also check the **Compute resources** settings. Contact your organization's AWS administrator if you don't have access to the AWS Console. +If your studio session doesn't advance from **starting** status to **running** status within 30 minutes, and you have access to the AWS Console for your organization, check that the AWS Batch compute environment associated with the Studio session is in the **ENABLED** state with a **VALID** status. You can also check the **Compute resources** settings. Contact your organization's AWS administrator if you don't have access to the AWS Console. If sufficient compute environment resources are unavailable, **Stop** the studio session and any others that may be running before trying again. If you have access to the AWS Console for your organization, you can terminate a specific session from the AWS Batch Jobs page (filtering by compute environment queue). From fde0a69e1107d3957a8f41d3cd4d8ca5d7676f3e Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 17:51:47 +0200 Subject: [PATCH 19/30] Fixed redirects --- static/_redirects | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/static/_redirects b/static/_redirects index 47b875c9c..98ac3ce78 100644 --- a/static/_redirects +++ b/static/_redirects @@ -24,12 +24,13 @@ /platform/24.2/faqs/* /platform/latest/troubleshooting_and_faqs/troubleshooting/:splat 301 # Redirect previous Data Studios content to new structure -/platform/24.1/data/data-studios /platform/latest/data_studios/ 301 -/platform/24.2/data/data-studios /platform/latest/data_studios/ 301 - -# Redirect all Data Studios content to Studios /platform/24.1/data/data-studios /platform/latest/studios/ 301 /platform/24.2/data/data-studios /platform/latest/studios/ 301 + +# Redirect all Data Studios content to Studios +/platform/24.1/data/data-studios /platform/latest/studios/* 301 +/platform/24.2/data/data-studios /platform/latest/studios/* 301 +/platform/24.3/data/data-studios /platform/latest/studios/* 301 /platform/latest/data-studios/* /platform/latest/studios/* 301 # Redirect first result on Google for CLI docs From ab6d14858632df5f07b90763d98552ff81492519 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 18:01:57 +0200 Subject: [PATCH 20/30] Redirect fixes --- static/_redirects | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/static/_redirects b/static/_redirects index 98ac3ce78..da1afe040 100644 --- a/static/_redirects +++ b/static/_redirects @@ -24,14 +24,15 @@ /platform/24.2/faqs/* /platform/latest/troubleshooting_and_faqs/troubleshooting/:splat 301 # Redirect previous Data Studios content to new structure -/platform/24.1/data/data-studios /platform/latest/studios/ 301 -/platform/24.2/data/data-studios /platform/latest/studios/ 301 +/platform/24.1/data/data_studios /platform/latest/studios/ 301 +/platform/24.2/data/data_studios /platform/latest/studios/ 301 # Redirect all Data Studios content to Studios -/platform/24.1/data/data-studios /platform/latest/studios/* 301 -/platform/24.2/data/data-studios /platform/latest/studios/* 301 -/platform/24.3/data/data-studios /platform/latest/studios/* 301 -/platform/latest/data-studios/* /platform/latest/studios/* 301 +/platform/24.1/data/data_studios /platform/latest/studios/* 301 +/platform/24.2/data/data_studios /platform/latest/studios/* 301 +/platform/24.3/data/data_studios /platform/latest/studios/* 301 +/platform/latest/data_studios/* /platform/latest/studios/* 301 +/platform/24.2/data/data_studios /platform/24.2/data_studios/ 301 # Redirect first result on Google for CLI docs /platform/23.3/cli /platform/latest/cli/overview/:splat 301 From faeffb7d1df014abf6163a28061b369f95bdcf1f Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 18:28:31 +0200 Subject: [PATCH 21/30] Redirects --- static/_redirects | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/static/_redirects b/static/_redirects index da1afe040..220ecbe36 100644 --- a/static/_redirects +++ b/static/_redirects @@ -28,11 +28,11 @@ /platform/24.2/data/data_studios /platform/latest/studios/ 301 # Redirect all Data Studios content to Studios -/platform/24.1/data/data_studios /platform/latest/studios/* 301 -/platform/24.2/data/data_studios /platform/latest/studios/* 301 -/platform/24.3/data/data_studios /platform/latest/studios/* 301 -/platform/latest/data_studios/* /platform/latest/studios/* 301 -/platform/24.2/data/data_studios /platform/24.2/data_studios/ 301 +/platform/24.1/data/data_studios/* /platform/latest/studios/:splat 301 +/platform/24.2/data/data_studios/* /platform/latest/studios/:splat 301 +/platform/24.3/data/data_studios/* /platform/latest/studios/:splat 301 +/platform/latest/data_studios/* /platform/latest/studios/:splat 301 +/platform/24.2/data/data_studios/* /platform/24.2/studios/:splat 301 # Redirect first result on Google for CLI docs /platform/23.3/cli /platform/latest/cli/overview/:splat 301 From fa0e0356b22b2fc3710e576ffb070cec12216133 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 20:20:55 +0200 Subject: [PATCH 22/30] Edits --- platform_versioned_docs/version-24.3/studios/index.mdx | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/platform_versioned_docs/version-24.3/studios/index.mdx b/platform_versioned_docs/version-24.3/studios/index.mdx index 64b3ad525..53941f721 100644 --- a/platform_versioned_docs/version-24.3/studios/index.mdx +++ b/platform_versioned_docs/version-24.3/studios/index.mdx @@ -7,7 +7,7 @@ tags: [studios] Studios is a unified platform where you can host a combination of container images and compute environments for interactive analysis using your preferred tools, like JupyterLab and RStudio Notebooks, Visual Studio Code IDEs, or Xpra remote desktops. Each Studio session is an individual interactive environment that encapsulates the live environment for dynamic data analysis. -On Seqera Cloud, the free tier permits only one running session at a time. To run simultaneous sessions, [contact Seqera][contact] for a Seqera Cloud Pro license. +On Seqera Cloud, the free tier permits only one running Studio session at a time. To run simultaneous sessions, [contact Seqera][contact] for a Seqera Cloud Pro license. :::note Studios is currently in **public preview** and is available from Seqera Platform v24.1. [Contact Seqera support](https://support.seqera.io) if you experience any problems during the deployment process. Studios in Enterprise is not enabled by default. You can enable Studios in the [environment variables configuration](../../version-24.2/enterprise/studios.mdx). @@ -23,7 +23,7 @@ Before you get started, you need the following: - [Data Explorer](../data/data-explorer.mdx) is enabled. :::note -Currently, Data Studios only supports AWS Batch compute environments that **do not** have Fargate enabled. +Currently, Studios only supports AWS Batch compute environments that **do not** have Fargate enabled. ::: ## Limitations @@ -58,7 +58,7 @@ Additionally, the Seqera Connect client version string has the format: When pushed to the container registry, an image template is tagged with the following tags: -- `-.`, such as `4.2.3-0.7`. When adding a new data studio container template image this is the tag displayed in Seqera Platform. +- `-.`, such as `4.2.3-0.7`. When adding a new Studio container template image this is the tag displayed in Seqera Platform. - `-..`, such as `4.2.3-0.7.1`. To view the latest versions of the images, see [public.cr.seqera.io](https://public.cr.seqera.io/). You can also augment the Seqera-provided image templates or use your own custom container image templates. This approach is recommended for managing reproducible analysis environments. For more information, see [Custom environments][custom-envs]. @@ -99,7 +99,7 @@ To see the list of all RStudio Server image templates available, see [public.cr. **Visual Studio Code 1.93.1** -[Visual Studio Code][def-vsc] is an integrated development environment (IDE) that supports many programming languages. The default user is the `root` account. The container template image ships with the latest stable version of [Nextflow] and the [VSCode extension for Nextflow][nf-lang-server] to make troubleshooting Nextflow workflows easier. To install additional extensions during a running session, select **Extensions**. Additional system-level packages can be installed in a terminal window using `apt install `. +[Visual Studio Code][def-vsc] is an integrated development environment (IDE) that supports many programming languages. The default user is the `root` account. The container template image ships with the latest stable version of [Nextflow] and the [VSCode extension for Nextflow][nf-lang-server] to make troubleshooting Nextflow workflows easier. To install additional extensions during a running Studio session, select **Extensions**. Additional system-level packages can be installed in a terminal window using `apt install `. To see the list of all Visual Studio Code image templates available, see [public.cr.seqera.io/platform/data-studio-vscode][ds-vscode]. @@ -107,7 +107,7 @@ To see the list of all Visual Studio Code image templates available, see [public [Xpra][def-xpra], known as _screen for X_, allows you to run X11 programs by giving you remote access to individual graphical applications. The container template image also installs NVIDIA Linux x64 (AMD64/EM64T) drivers for Ubuntu 22.04 for running GPU-enabled applications. To use these GPU drivers, your compute environment must specify GPU instance families. -The default user is the `root` account. The image is based on `ubuntu:jammy`. Additional system-level packages can be installed during a running session in a terminal window using `apt install `. +The default user is the `root` account. The image is based on `ubuntu:jammy`. Additional system-level packages can be installed during a running Studio session in a terminal window using `apt install `. To see the list of all Xpra image templates available, see [public.cr.seqera.io/repo/platform/data-studio-xpra][ds-xpra]. From c4025e6668191217947f810db7b4bf54f754cbaa Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 21:35:38 +0200 Subject: [PATCH 23/30] Rewording --- .../version-24.3/studios/index.mdx | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/platform_versioned_docs/version-24.3/studios/index.mdx b/platform_versioned_docs/version-24.3/studios/index.mdx index 53941f721..dc2782d1b 100644 --- a/platform_versioned_docs/version-24.3/studios/index.mdx +++ b/platform_versioned_docs/version-24.3/studios/index.mdx @@ -34,7 +34,7 @@ For more information on AWS Batch configuration, see [AWS Batch][aws-batch]. ## Container image templates -Studios provides four container image templates: JupyterLab, RStudio Server, Visual Studio Code, and Xpra. The image templates install a very limited number of packages when the session container is built. You can install additional packages as needed during a session. +There are four container image templates provided: JupyterLab, RStudio Server, Visual Studio Code, and Xpra. The image templates install a very limited number of packages when the Studio session container is built. You can install additional packages as needed during a Studio session. The image template tag includes the version of the analysis application, an optional incompatibility flag, and the Seqera Connect version. Connect is the proprietary Seqera web server client that manages communication with the container. The tag string looks like this: @@ -87,13 +87,13 @@ The default user is the `root` account. The following [conda-forge](https://cond - `nb_black=1.0.7` - `qgrid=1.3.1` -To install additional Python packages during a running session, execute `!pip install ` commands in your notebook environment. Additional system-level packages can be installed in a terminal window using `apt install `. +To install additional Python packages during a running Studio session, execute `!pip install ` commands in your notebook environment. Additional system-level packages can be installed in a terminal window using `apt install `. To see the list of all JupyterLab image templates available, see [public.cr.seqera.io/repo/platform/data-studio-jupyter][ds-jupyter]. **RStudio Server 4.4.1** -The default user is the `root` account. To install R packages during a running session, execute `install.packages("")` commands in your notebook environment. Additional system-level packages can be installed in a terminal window using `apt install `. +The default user is the `root` account. To install R packages during a running Studio session, execute `install.packages("")` commands in your notebook environment. Additional system-level packages can be installed in a terminal window using `apt install `. To see the list of all RStudio Server image templates available, see [public.cr.seqera.io/repo/platform/data-studio-rstudio][ds-rstudio]. @@ -111,7 +111,7 @@ The default user is the `root` account. The image is based on `ubuntu:jammy`. Ad To see the list of all Xpra image templates available, see [public.cr.seqera.io/repo/platform/data-studio-xpra][ds-xpra]. -## Session statuses +## Studio session statuses Studios have the following possible statuses: @@ -127,7 +127,7 @@ Studios have the following possible statuses: If you encounter an error with the public preview release of Studios, [contact Seqera support][contact]. ::: -## Session data links +## Studio session data links You can configure a Studio to mount one or more data links, where cloud buckets that you have configured in your compute environment are read-only, or read-write available to the session. @@ -142,11 +142,11 @@ Mounted data links are exposed at the `/workspace/data/` directory path inside a For more information, see [Limit Studio access to a specific cloud bucket subdirectory][cloud-bucket-subdirectory]. -## Session checkpoints +## Studio session checkpoints When starting a Studio session, a *checkpoint* is automatically created. A checkpoint saves all changes made to the root filesystem and stores it in the attached compute environment's pipeline work directory in the `.studios/checkpoints` folder with a unique name. The current checkpoint is updated every five minutes during a session. -When you stop and start a Studio session, or start a new Studio session from a previously created checkpoint, changes such as installed software packages and configuration files are restored and made available in the Studio session. Changes made to mounted data are not included in a checkpoint. +When you stop and start a Studio session, or start a new one from a previously created checkpoint, changes such as installed software packages and configuration files are restored and made available in the Studio session. Changes made to mounted data are not included in a checkpoint. Checkpoints can be renamed and the name has to be unique per Studio. Spaces in checkpoint names are converted to underscores automatically. From e6c3d25920ac00bce78a1be4fed5f893201d4c2f Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Wed, 19 Feb 2025 22:51:12 +0200 Subject: [PATCH 24/30] Rewording --- platform_versioned_docs/version-24.3/studios/index.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_docs/version-24.3/studios/index.mdx b/platform_versioned_docs/version-24.3/studios/index.mdx index dc2782d1b..9e51f0c7b 100644 --- a/platform_versioned_docs/version-24.3/studios/index.mdx +++ b/platform_versioned_docs/version-24.3/studios/index.mdx @@ -146,7 +146,7 @@ For more information, see [Limit Studio access to a specific cloud bucket subdir When starting a Studio session, a *checkpoint* is automatically created. A checkpoint saves all changes made to the root filesystem and stores it in the attached compute environment's pipeline work directory in the `.studios/checkpoints` folder with a unique name. The current checkpoint is updated every five minutes during a session. -When you stop and start a Studio session, or start a new one from a previously created checkpoint, changes such as installed software packages and configuration files are restored and made available in the Studio session. Changes made to mounted data are not included in a checkpoint. +When you stop and start a Studios session, or start a new session from a previously created checkpoint, changes such as installed software packages and configuration files are restored and made available. Changes made to mounted data are not included in a checkpoint. Checkpoints can be renamed and the name has to be unique per Studio. Spaces in checkpoint names are converted to underscores automatically. From efa819cb44f2de75b68dde9469d5a9b1abcfce99 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 25 Feb 2025 21:24:49 +0200 Subject: [PATCH 25/30] Apply suggestions from code review Co-authored-by: Chris Hakkaart Co-authored-by: Rob Newman <61608+robnewman@users.noreply.github.com> Signed-off-by: Justine Geffen --- .../version-24.2/enterprise/studios.mdx | 2 +- .../version-24.3/cli/commands.mdx | 2 +- .../version-24.3/getting-started/proteinfold.mdx | 2 +- .../version-24.3/studios/index.mdx | 14 +++++++------- .../version-24.3/studios/managing.mdx | 14 +++++++------- .../studios_troubleshooting.mdx | 8 ++++---- 6 files changed, 21 insertions(+), 21 deletions(-) diff --git a/platform_versioned_docs/version-24.2/enterprise/studios.mdx b/platform_versioned_docs/version-24.2/enterprise/studios.mdx index 41a612fa2..dcc79dfd9 100644 --- a/platform_versioned_docs/version-24.2/enterprise/studios.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/studios.mdx @@ -5,7 +5,7 @@ date: "12 Jun 2024" tags: [docker, compose, kubernetes, data, studios, deployment] --- -Enable Studios as part of your Seqera Platform instance. You must have Data Explorer enabled to use Data Studios. Only the Amazon AWS public cloud is currently supported. +Enable Studios as part of your Seqera Platform instance. You must have Data Explorer enabled to use Studios. Only the Amazon AWS public cloud is currently supported. :::caution You must complete the upgrade of your Platform Enterprise installation to version 24.1.4 before enabling and configuring Data Studios. diff --git a/platform_versioned_docs/version-24.3/cli/commands.mdx b/platform_versioned_docs/version-24.3/cli/commands.mdx index d925bbfe6..34012d302 100644 --- a/platform_versioned_docs/version-24.3/cli/commands.mdx +++ b/platform_versioned_docs/version-24.3/cli/commands.mdx @@ -272,7 +272,7 @@ https://api.cloud.seqera.io/workspaces/97652229034xxx/datasets/6vBGj6aWWpBuLpGKj Run `tw studios -h` to view the list of supported operations. -Manage [Studio sessions](../studios/index.mdx) hosted in Seqera Platform. Studio sessions allow interactive analysis using Jupyter, RStudio, VSCode, and Xpra. Additional custom analysis environments can be defined as needed. +Manage [Studio sessions](../studios/index.mdx) hosted in Seqera Platform. Studio sessions allow interactive analysis using Jupyter, RStudio, VS Code, and Xpra. Additional custom analysis environments can be defined as needed. :::note Most Studio operations require workspace `MAINTAIN` permissions. diff --git a/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx b/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx index 4f44a2c31..4da720454 100644 --- a/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx +++ b/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx @@ -308,7 +308,7 @@ After you have filled the necessary launch details, select **Launch**. The **Run ## Interactive analysis with Studios -[Studios](../studios/index.mdx) streamlines the process of creating interactive analysis environments for Platform users. With built-in templates for platforms like Jupyter Notebook, RStudio, and VSCode, creating a data studio is as simple as adding and sharing pipelines or datasets. The Studio URL can also be shared with any user with the [Connect role](../orgs-and-teams/roles.mdx) for real-time access and collaboration. +[Studios](../studios/index.mdx) streamlines the process of creating interactive analysis environments for Platform users. With built-in templates for platforms like Jupyter Notebook, RStudio, and VS Code, creating a data studio is as simple as adding and sharing pipelines or datasets. The Studio URL can also be shared with any user with the [Connect role](../orgs-and-teams/roles.mdx) for real-time access and collaboration. For the purposes of this guide, a Jupyter notebook environment will be used for interactive visualization of the predicted protein structures, optionally comparing AlphaFold2 and Colabfold structures for the same sequence data. diff --git a/platform_versioned_docs/version-24.3/studios/index.mdx b/platform_versioned_docs/version-24.3/studios/index.mdx index 9e51f0c7b..d153309f1 100644 --- a/platform_versioned_docs/version-24.3/studios/index.mdx +++ b/platform_versioned_docs/version-24.3/studios/index.mdx @@ -58,7 +58,7 @@ Additionally, the Seqera Connect client version string has the format: When pushed to the container registry, an image template is tagged with the following tags: -- `-.`, such as `4.2.3-0.7`. When adding a new Studio container template image this is the tag displayed in Seqera Platform. +- `-.`, such as `4.2.3-0.7`. When adding a new container template image this is the tag displayed in Seqera Platform. - `-..`, such as `4.2.3-0.7.1`. To view the latest versions of the images, see [public.cr.seqera.io](https://public.cr.seqera.io/). You can also augment the Seqera-provided image templates or use your own custom container image templates. This approach is recommended for managing reproducible analysis environments. For more information, see [Custom environments][custom-envs]. @@ -99,7 +99,7 @@ To see the list of all RStudio Server image templates available, see [public.cr. **Visual Studio Code 1.93.1** -[Visual Studio Code][def-vsc] is an integrated development environment (IDE) that supports many programming languages. The default user is the `root` account. The container template image ships with the latest stable version of [Nextflow] and the [VSCode extension for Nextflow][nf-lang-server] to make troubleshooting Nextflow workflows easier. To install additional extensions during a running Studio session, select **Extensions**. Additional system-level packages can be installed in a terminal window using `apt install `. +[Visual Studio Code][def-vsc] is an integrated development environment (IDE) that supports many programming languages. The default user is the `root` account. The container template image ships with the latest stable version of [Nextflow] and the [VS Code extension for Nextflow][nf-lang-server] to make troubleshooting Nextflow workflows easier. To install additional extensions during a running Studio session, select **Extensions**. Additional system-level packages can be installed in a terminal window using `apt install `. To see the list of all Visual Studio Code image templates available, see [public.cr.seqera.io/platform/data-studio-vscode][ds-vscode]. @@ -113,14 +113,14 @@ To see the list of all Xpra image templates available, see [public.cr.seqera.io/ ## Studio session statuses -Studios have the following possible statuses: +Sessions have the following possible statuses: - **building**: When a custom environment is building the template image for a new Studio session. The [Wave] service performs the build action. For more information on this status, see [Inspect custom container template build status][build-status]. - **build-failed**: When a custom environment build has failed. This is a non-recoverable error. Logs are provided to assist with troubleshooting. For more information on this status, see [Inspect custom container template build status][build-status]. - **starting**: The Studio is initializing. - **running**: When a Studio session is **running**, you can connect to it, copy the URL, or stop it. In addition, the session can continue to process requests/run computations in the absence of an ongoing connection. -- **stopping**: The recently-running session is in the process of being stopped. -- **stopped**: When a session is stopped, the associated compute resources are deallocated. You can start or delete the Studio when it's in this state. +- **stopping**: The recently-running Studio session is in the process of being stopped. +- **stopped**: When a Studio session is stopped, the associated compute resources are deallocated. You can start or delete the session when it's in this state. - **errored**: This state most often indicates that there has been an error starting the Studio session but it is in a **stopped** state. There might be errors reported by the session itself but these will be overwritten with a **running** status if the session is still running. :::tip @@ -129,7 +129,7 @@ Studios have the following possible statuses: ## Studio session data links -You can configure a Studio to mount one or more data links, where cloud buckets that you have configured in your compute environment are read-only, or read-write available to the session. +You can configure a Studio session to mount one or more data links, where cloud buckets that you have configured in your compute environment are read-only, or read-write available to the session. If your compute environment includes a cloud bucket in the **Allowed S3 bucket** list, the bucket is writeable from within a session when that bucket is included as a data link. @@ -166,7 +166,7 @@ The maximum storage allocation for a session is limited by the compute environme If the maximum allocation size is reached, it is possible to reclaim storage space using a snapshot. -Stop the active session to trigger a snapshot from the active volume. Studios uploads the snapshot to cloud storage with Fusion. When you start from the newly saved snapshot, all previous data is loaded and the newly-started session will have 2 GB of available space. +Stop the active session to trigger a snapshot from the active volume. The snapshot is uploaded to cloud storage with Fusion. When you start from the newly saved snapshot, all previous data is loaded, and the newly started session will have 2 GB of available space. {/* links */} [contact]: https://support.seqera.io/ diff --git a/platform_versioned_docs/version-24.3/studios/managing.mdx b/platform_versioned_docs/version-24.3/studios/managing.mdx index 9e2fb2f37..2bdaf86f6 100644 --- a/platform_versioned_docs/version-24.3/studios/managing.mdx +++ b/platform_versioned_docs/version-24.3/studios/managing.mdx @@ -34,7 +34,7 @@ To add a new Studio, complete the following steps: - To use one of the Seqera-provided container templates, complete the following steps: 1. Customize the following fields: - - **Container template**: Select a Studio template from the dropdown list. + - **Container template**: Select a template from the dropdown list. - **Studio name** - Optional: **Description** 1. Optional: Select **Install Conda packages** to enter or upload a list of Conda packages to include with the Studio. For more information on the syntax for specifying Conda packages, see [Conda package syntax][conda-syntax]. @@ -59,7 +59,7 @@ To add a new Studio, complete the following steps: - If you want to save the Studio for future use, select **Add only**. - If you want to save and immediately start the Studio, select **Add and start**. -You'll be returned to the Studios landing page that displays the list of Studio sessions in your workspace. You can inspect the configuration details of the session that you created by selecting the session name. The Studio that you created will be listed with a status of either **stopped** or **starting**, depending on whether you elected to only add it or to start a session as well. +You'll be returned to the Studios landing page that displays the list of Studio sessions in your workspace. Select a Studio to inspect its configuration details. The Studio you created will be listed with a status of either **stopped** or **starting**, based on whether you elected to **Add** it or to **Add and start** a session as well. :::note By default, sessions only have read permissions to mounted data paths. Write permissions can be added for specific cloud storage buckets during the compute environment configuration by defining additional **Allowed S3 Buckets**. This means that data can be written from the session back to the cloud storage path(s) mounted. To stop potential data loss, only one session per workspace can mount a unique data path. When adding a new session, data paths already mounted to other running sessions are unavailable. If a new file is uploaded to the cloud storage bucket path while a session is running, the file may not be available to the session immediately. @@ -69,23 +69,23 @@ By default, sessions only have read permissions to mounted data paths. Write per This functionality is available to users with the **Maintain** role and above. -A Studio needs to be started before you can connect to it. Select the three dots next to the status message for the Studio you want to start, then select **Start**. You can optionally change the configuration of the Studio, then select **Start in new tab**. A new browser tab will open that displays the startup state of the session. Once the session is running, you can connect to it. A session will run until it is stopped manually or it encounters a technical issue. +A Studio session needs to be started before you can connect to it. Select the three dots next to the status message for the Studio you want to start, then select **Start**. You can optionally change the configuration of the Studio, then select **Start in new tab**. A new browser tab will open that displays the startup state of the session. Once the session is running, you can connect to it. A session will run until it is stopped manually or it encounters a technical issue. :::note A session consumes resources until it's **stopped**. ::: -Once a session is in a **running** state, you can connect to it, obtain the public link to the session to share with collaborators inside your workspace, and stop it. +Once a Studio session is in a **running** state, you can connect to it, obtain a public link to the session to share with collaborators inside your workspace, and stop it. ## Start an existing Studio as a new session This functionality is available to users with the **Maintain** role and above. -You can use any existing Studio as the foundation for adding a new Studio. This functionality creates a clone of the Studio, including its checkpoint history, preserving any modifications made to the original Studio. When you create a session in this way, future changes are isolated from the original session. +You can use any existing Studio as the foundation for adding a new session. This functionality creates a clone of the session, including its checkpoint history, preserving any modifications made to the original Studio. When you create a session in this way, future changes are isolated from the original session. When adding a new session from an existing session or checkpoint, the following fields cannot be changed: -- **Studio Template** +- **Studio template** - **Original Studio session and checkpoint** - **Compute environment** - **Installed Conda packages** @@ -106,7 +106,7 @@ An active connection to a session will not prevent administrative actions that m Once connected, the session will display the status of **running** in the list, and any connected user's avatar will be displayed under the status in both the list of Studios and in each Studio's detail page. -## Collaborate in a Studio +## Collaborate in a Studio session This functionality is available to all user roles excluding the **View** role. diff --git a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx index 3cf6d441e..5ef9ece8d 100644 --- a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx +++ b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx @@ -27,13 +27,13 @@ If you're not able to stop a session, it's usually because the Batch job running ## Studio session performance is poor -A slow or unresponsive session may be due to its AWS Batch compute environment being utilized for other jobs, such as running Nextflow pipelines. The compute environment is responsible for scheduling jobs to the available compute resources. Studio sessions compete for resources with the Nextflow pipeline head job and Seqera does not currently have an established pattern of precedence. +A slow or unresponsive Studio session may be due to its AWS Batch compute environment being utilized for other jobs, such as running Nextflow pipelines. The compute environment is responsible for scheduling jobs to the available compute resources. Studio sessions compete for resources with the Nextflow pipeline head job and Seqera does not currently have an established pattern of precedence. If you have access to the AWS Console for your organization, check the jobs associated with the AWS Batch compute environment and compare the resources allocated with its **Compute resources** settings. ## Memory allocation of the Studio session is exceeded -The running container in the AWS Batch compute environment inherits the memory limits specified by the studio session configuration when adding or starting the session. The kernel then handles the memory as if running natively on Linux. Linux can overcommit memory, leading to possible out-of-memory errors in a container environment. The kernel has protections in place to prevent this, but it can happen, and in this case, the process is killed. This can manifest as a performance lag, killed subprocesses, or at worst, a killed session. Running sessions have automated snapshots created every five minutes, so if the running container is killed only those changes made after the prior snapshot creation will be lost. +The running container in the AWS Batch compute environment inherits the memory limits specified by the session configuration when adding or starting the session. The kernel then handles the memory as if running natively on Linux. Linux can overcommit memory, leading to possible out-of-memory errors in a container environment. The kernel has protections in place to prevent this, but it can happen, and in this case, the process is killed. This can manifest as a performance lag, killed subprocesses, or at worst, a killed session. Running sessions have automated snapshots created every five minutes, so if the running container is killed only those changes made after the prior snapshot creation will be lost. ## All datasets are read-only @@ -56,9 +56,9 @@ This is displayed because logging is set to `stderr` by default to ensure all lo ## Container template image security scan false positives -### VSCode +### VS Code -When running an SCA security scan (e.g., with Trivy) on the latest Seqera-provided VSCode image [container template](../studios#container-image-templates), you may encounter multiple false-positive findings. This issue is due to how VSCode defines extensions, which can cause certain security scanners to incorrectly identify them as `npm` packages. +When running an SCA security scan (e.g., with Trivy) on the latest Seqera-provided VS Code image [container template](../studios#container-image-templates), you may encounter multiple false-positive findings. This issue is due to how VS Code defines extensions, which can cause certain security scanners to incorrectly identify them as `npm` packages. This is a known limitation and has been discussed in the Trivy community [here(https://github.com/aquasecurity/trivy/discussions/6112)]. From 8b23fefab7a11efda2878cad873c3ccf6d4f2348 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 25 Feb 2025 21:25:35 +0200 Subject: [PATCH 26/30] Update platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx Signed-off-by: Justine Geffen --- .../troubleshooting_and_faqs/studios_troubleshooting.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx index 5ef9ece8d..f56e0bf18 100644 --- a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx +++ b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx @@ -15,7 +15,7 @@ In your interactive analysis environment, open a new terminal and type `ls -la / If your studio session doesn't advance from **starting** status to **running** status within 30 minutes, and you have access to the AWS Console for your organization, check that the AWS Batch compute environment associated with the Studio session is in the **ENABLED** state with a **VALID** status. You can also check the **Compute resources** settings. Contact your organization's AWS administrator if you don't have access to the AWS Console. -If sufficient compute environment resources are unavailable, **Stop** the studio session and any others that may be running before trying again. If you have access to the AWS Console for your organization, you can terminate a specific session from the AWS Batch Jobs page (filtering by compute environment queue). +If sufficient compute environment resources are unavailable, **Stop** the session and any others that may be running before trying again. If you have access to the AWS Console for your organization, you can terminate a specific session from the AWS Batch Jobs page (filtering by compute environment queue). ## Studio session status is **errored** From 3a81fc71231e6fd5c332ff83d4015a35ee7918df Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 25 Feb 2025 22:30:42 +0200 Subject: [PATCH 27/30] Additional renaming and fixing --- .../configtables/data_features_env.yml | 8 ++-- .../enterprise/docker-compose.mdx | 4 +- .../version-24.2/enterprise/kubernetes.mdx | 2 +- .../version-24.2/enterprise/studios.mdx | 10 ++--- .../version-24.3/compute-envs/aws-batch.mdx | 2 +- .../getting-started/proteinfold.mdx | 12 ++--- .../version-24.3/getting-started/rnaseq.mdx | 44 +++++++++---------- .../version-24.3/getting-started/studios.mdx | 18 ++++---- .../monitoring/configtables/log_events.yml | 4 +- .../version-24.3/orgs-and-teams/roles.mdx | 8 ++-- .../version-24.3/studios/custom-envs.mdx | 2 +- .../version-24.3/studios/index.mdx | 20 ++++----- .../version-24.3/studios/managing.mdx | 14 +++--- .../studios_troubleshooting.mdx | 26 ++++++----- 14 files changed, 85 insertions(+), 89 deletions(-) diff --git a/platform_versioned_docs/version-24.2/enterprise/configuration/configtables/data_features_env.yml b/platform_versioned_docs/version-24.2/enterprise/configuration/configtables/data_features_env.yml index 8b9ed6886..3d245e736 100644 --- a/platform_versioned_docs/version-24.2/enterprise/configuration/configtables/data_features_env.yml +++ b/platform_versioned_docs/version-24.2/enterprise/configuration/configtables/data_features_env.yml @@ -2,7 +2,7 @@ - Environment variable: '`TOWER_DATA_EXPLORER_ENABLED`' Description: > - Enable [Data Explorer](https://docs.seqera.io/platform/latest/data/data-explorer) in all workspaces. To mount data inside a data studio, you must enable Data Explorer. + Enable [Data Explorer](https://docs.seqera.io/platform/latest/data/data-explorer) in all workspaces. To mount data inside a Studio, you must enable Data Explorer. Value: 'Default: `false`' - Environment variable: '`TOWER_DATA_EXPLORER_CLOUD_DISABLED_WORKSPACES`' @@ -32,15 +32,15 @@ - Environment variable: '`TOWER_DATA_STUDIO_CONNECT_URL`' Description: > - The URL of the Data Studios connect proxy. The connect proxy is used internally by Seqera Platform. See [Data Studios deployment](https://docs.seqera.io/platform/latest/enterprise/data-studios). + The URL of the Studios connect proxy. The connect proxy is used internally by Seqera Platform. See [Studios deployment](https://docs.seqera.io/platform/latest/enterprise/studios). Value: 'Example: `https://connect.example.com/`' - Environment variable: '`TOWER_OIDC_REGISTRATION_INITIAL_ACCESS_TOKEN`' Description: > - An access token used to register new clients in Seqera Platform. Any alphanumeric value is allowed. See [Data Studios deployment](https://docs.seqera.io/platform/latest/enterprise/data-studios). + An access token used to register new clients in Seqera Platform. Any alphanumeric value is allowed. See [Studios deployment](https://docs.seqera.io/platform/latest/enterprise/studios). Value: 'd5XDoRzHpWo1c............mDnfBpB' - Environment variable: '`TOWER_OIDC_PEM_PATH`' Description: > - The file path to a PEM certificate used to sign the OIDC tokens for the OpenID connect provider. See [Data Studios deployment](https://docs.seqera.io/platform/latest/enterprise/data-studios). + The file path to a PEM certificate used to sign the OIDC tokens for the OpenID connect provider. See [Studios deployment](https://docs.seqera.io/platform/latest/enterprise/studios). Value: 'Example: `/data-studios-rsa.pem`' diff --git a/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx b/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx index 4f6d4b59b..714bf3e4d 100644 --- a/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx @@ -25,7 +25,7 @@ The DB or Redis volume is persistent after a Docker restart by default. Use the - To configure the Seqera pipeline resource optimization service (`groundswell`), see [Pipeline resource optimization](./configuration/pipeline_optimization.mdx). - - To deploy with Studios, see [Data studios deployment](../enterprise/studios.mdx). + - To deploy with Studios, see [Studios deployment](../enterprise/studios.mdx). 4. Deploy the application and wait for it to initialize (this process takes a few minutes): @@ -45,7 +45,7 @@ For more information on configuration, see [Configuration options](./configurati ### Studios -[Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](./studios.mdx). +[Studios](../studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](./studios.mdx). :::note Studios is currently in **public preview** and is available from Seqera Platform v24.1. If you experience any problems during the deployment process please contact your account executive. Data Studios in Enterprise is not installed by default. diff --git a/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx b/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx index 5d8fbf3fe..b5b0fe62b 100644 --- a/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx @@ -252,7 +252,7 @@ The initContainers will wait until both the Seqera and pipeline optimization ser ### Studios -[Data Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Data Studios, see [Studios deployment](./studios.mdx). +[Studios](../studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](./studios.mdx). :::note Studios is currently in **public preview** and is available from Seqera Platform v24.1. If you experience any problems during the deployment process [contact Seqera support](https://support.seqera.io). Studios in Enterprise is not installed by default. diff --git a/platform_versioned_docs/version-24.2/enterprise/studios.mdx b/platform_versioned_docs/version-24.2/enterprise/studios.mdx index dcc79dfd9..8311f52ef 100644 --- a/platform_versioned_docs/version-24.2/enterprise/studios.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/studios.mdx @@ -8,7 +8,7 @@ tags: [docker, compose, kubernetes, data, studios, deployment] Enable Studios as part of your Seqera Platform instance. You must have Data Explorer enabled to use Studios. Only the Amazon AWS public cloud is currently supported. :::caution -You must complete the upgrade of your Platform Enterprise installation to version 24.1.4 before enabling and configuring Data Studios. +You must complete the upgrade of your Platform Enterprise installation to version 24.1.4 before enabling and configuring Studios. ::: ## DNS configuration @@ -20,7 +20,7 @@ Provide a wildcard TLS certificate to allow for uniquely generated subdomains. A Studios uses the following set of domains and subdomains: - The domain that you set for `TOWER_SERVER_URL`, such as `example.com`. -- A wildcard subdomain that you must configure specifically for Studios. This wildcard subdomain is the parent for each unique Studios session URL, such as `abcd.example.com`. +- A wildcard subdomain that you must configure specifically for Studios. This wildcard subdomain is the parent for each unique session URL, such as `abcd.example.com`. - The connection proxy, defined by `CONNECT_PROXY_URL`. This URL is a first-level subdomain of your `TOWER_SERVER_URL`. For example, `https://connect.example.com`. ## Studios workspace availability @@ -33,7 +33,7 @@ You can configure which organizational workspaces have access to Studios. This c ## Available Studio environment images -Each of the provided Studios environments includes a particular version of the underlying data analytics software package. +Each of the provided environments includes a particular version of the underlying data analytics software package. To quickly identify which version of the software an image includes, the version string for each container is in the form of `-`. For example, if the version string for the RStudio Server is `4.4.1-0.7.4`, version `4.4.1` is the RStudio version and `0.7.4` is the version of this Seqera-built container image. @@ -78,7 +78,7 @@ This guide assumes that all services will be run in the same container as the re ```yaml volumes: - $PWD/tower.yml:/tower.yml - # An RSA key is required for Data Studios functionality. Uncomment the line below to mount the key. + # An RSA key is required for Studios functionality. Uncomment the line below to mount the key. #- $PWD/data-studios-rsa.pem:/data-studios-rsa.pem ``` @@ -143,7 +143,7 @@ This procedure describes how to configure Studios for Kubernetes deployments of 1. Edit the `proxy.yml` file and set the following variables: - `CONNECT_REDIS_ADDRESS`: The hostname or IP address of the Redis server configured for Platform. - - `CONNECT_PROXY_URL`: A URL for the connect proxy subdomain. We recommend you set a first-level subdomain of your Platform installation domain (`PLATFORM_URL` below) for your connect proxy, to be able to use the same wildcard TLS certificate for all Studio session URLs and avoid additional domain nesting. For example, `https://connect.example.com`. + - `CONNECT_PROXY_URL`: A URL for the connect proxy subdomain. We recommend you set a first-level subdomain of your Platform installation domain (`PLATFORM_URL` below) for your connect proxy, to be able to use the same wildcard TLS certificate for all session URLs and avoid additional domain nesting. For example, `https://connect.example.com`. - `PLATFORM_URL`: The base URL for your Platform installation, such as `https://example.com/`. - `CONNECT_OIDC_CLIENT_REGISTRATION_TOKEN`: The same value as the `oidc_registration_token` value created previously. diff --git a/platform_versioned_docs/version-24.3/compute-envs/aws-batch.mdx b/platform_versioned_docs/version-24.3/compute-envs/aws-batch.mdx index 0d3d883cc..62b7b3a50 100644 --- a/platform_versioned_docs/version-24.3/compute-envs/aws-batch.mdx +++ b/platform_versioned_docs/version-24.3/compute-envs/aws-batch.mdx @@ -41,7 +41,7 @@ We recommend that you create separate IAM policies for Batch Forge and launch pe 1. To create a Launch user, you must also create the [S3 bucket write policy](https://github.com/seqeralabs/nf-tower-aws/blob/master/launch/s3-bucket-write.json) separately to attach to your Launch user. -1. To use Data Explorer and Data Studios, you must create the [Data policy](https://github.com/seqeralabs/nf-tower-aws/blob/master/data/data-explorer-policy.json) separately to attach to your Platform users. +1. To use Data Explorer and Studios, you must create the [Data policy](https://github.com/seqeralabs/nf-tower-aws/blob/master/data/data-explorer-policy.json) separately to attach to your Platform users. 1. Select **Next: Tags**. 1. Select **Next: Review**. diff --git a/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx b/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx index 4da720454..812770955 100644 --- a/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx +++ b/platform_versioned_docs/version-24.3/getting-started/proteinfold.mdx @@ -2,7 +2,7 @@ title: "Protein structure prediction" description: "An introduction to running nf-core/proteinfold in Seqera Platform" date: "21 Jul 2024" -tags: [platform, seqera pipelines, data studios, proteinfold, alphafold, colabfold, compute environment, aws] +tags: [platform, seqera pipelines, studios, proteinfold, alphafold, colabfold, compute environment, aws] toc_max_heading_level: 2 --- @@ -15,7 +15,7 @@ This guide details how to perform best-practice analysis for protein 3D structur - Adding the nf-core/proteinfold pipeline to your workspace - Importing your pipeline input data - Launching the pipeline and monitoring execution from your workspace -- Setting up a custom analysis environment with Data Studios +- Setting up a custom analysis environment with Studios :::info[**Prerequisites**] You will need the following to get started: @@ -53,7 +53,7 @@ Fusion requires a license for use in Seqera Platform compute environments or dir ### Create compute environment :::info -The same compute environment can be used for pipeline execution and running your Data Studios notebook environment, but Data Studios does not support AWS Fargate. To use this compute environment for both nf-core/proteinfold execution and your data studio, leave **Enable Fargate for head job** disabled and include a CPU-based EC2 instance family (`c6id`, `r6id`, etc.) in your **Instance types**. +The same compute environment can be used for pipeline execution and running your Studios notebook environment, but Studios does not support AWS Fargate. To use this compute environment for both nf-core/proteinfold execution and your data studio, leave **Enable Fargate for head job** disabled and include a CPU-based EC2 instance family (`c6id`, `r6id`, etc.) in your **Instance types**. Alternatively, create a second basic AWS Batch compute environment and a data studio with at least 2 CPUs and 8192 MB of RAM. ::: @@ -75,10 +75,10 @@ From the **Compute Environments** tab in your organization workspace, select **A | **Config Mode** | Batch Forge | | **Provisioning Model** | Choose between Spot and On-demand instances. | | **Max CPUs** | Sensible values for production use range between 2000 and 5000.| -| **Enable Fargate for head job** | Run the Nextflow head job using the Fargate container service to speed up pipeline launch. Requires Fusion v2. Do not enable for Data Studios compute environments. | +| **Enable Fargate for head job** | Run the Nextflow head job using the Fargate container service to speed up pipeline launch. Requires Fusion v2. Do not enable for Studios compute environments. | | **Use Amazon-recommended GPU-optimized ECS AMI** | When enabled, Batch Forge specifies the most current AWS-recommended GPU-optimized ECS AMI as the EC2 fleet AMI when creating the compute environment. | | **Allowed S3 buckets** | Additional S3 buckets or paths to be granted read-write permission for this compute environment. For the purposes of this guide, add `s3://proteinfold-dataset` to grant compute environment access to the DB and params used for prediction by AlphaFold2 and ColabFold. | -| **Instance types** | Specify the instance types to be used for computation. You must include GPU-enabled instance types (`g4dn`, `g5`) when the Amazon-recommended GPU-optimized ECS AMI is in use. Include CPU-based instance families for Data Studios compute environments. | +| **Instance types** | Specify the instance types to be used for computation. You must include GPU-enabled instance types (`g4dn`, `g5`) when the Amazon-recommended GPU-optimized ECS AMI is in use. Include CPU-based instance families for Studios compute environments. | | **Resource labels** | `name=value` pairs to tag the AWS resources created by this compute environment.| ![Create AWS Batch compute environment](./_images/pf-ce.gif) @@ -324,7 +324,7 @@ From the **Studios** tab, select **Add a Studio** and complete the following: ::: - Optional: Enter CPU and memory allocations. The default values are 2 CPUs and 8192 MB memory (RAM). :::note - Data studios compete for computing resources when sharing compute environments. Ensure your compute environment has sufficient resources to run both your pipelines and data studio sessions. + Studios compete for computing resources when sharing compute environments. Ensure your compute environment has sufficient resources to run both your pipelines and data studio sessions. ::: - Mount data using Data Explorer: Mount the S3 bucket or directory path that contains the pipeline work directory of your Proteinfold run. - In the **General config** tab: diff --git a/platform_versioned_docs/version-24.3/getting-started/rnaseq.mdx b/platform_versioned_docs/version-24.3/getting-started/rnaseq.mdx index 63d7eba85..fa5c7e038 100644 --- a/platform_versioned_docs/version-24.3/getting-started/rnaseq.mdx +++ b/platform_versioned_docs/version-24.3/getting-started/rnaseq.mdx @@ -2,7 +2,7 @@ title: "RNA-Seq" description: "An introduction to running nf-core/rnaseq in Seqera Platform" date: "21 Jul 2024" -tags: [platform, seqera pipelines, data studios, rnaseq, compute environment, aws] +tags: [platform, seqera pipelines, studios, rnaseq, compute environment, aws] toc_max_heading_level: 2 --- @@ -15,7 +15,7 @@ This guide details how to run bulk RNA sequencing (RNA-Seq) data analysis, from - Adding pipelines to your workspace - Importing your pipeline input data - Launching the pipeline and monitoring execution from your workspace -- Setting up a custom analysis environment with Data Studios +- Setting up a custom analysis environment with Studios - Resource allocation guidance for RNA-Seq data :::info[**Prerequisites**] @@ -30,7 +30,7 @@ You will need the following to get started: Compute and storage requirements for RNA-Seq analysis are dependent on the number of samples and the sequencing depth of your input data. See [RNA-Seq data and requirements](#rna-seq-data-and-requirements) for details on RNA-Seq datasets and the CPU and memory requirements for important steps of RNA-Seq pipelines. -In this guide, you will create an AWS Batch compute environment with sufficient resources allocated to run the [nf-core/rnaseq](https://github.com/nf-core/rnaseq) pipeline with a large dataset. This compute environment will also be used to run a Data Studios RStudio environment for interactive analysis of the resulting pipeline data. +In this guide, you will create an AWS Batch compute environment with sufficient resources allocated to run the [nf-core/rnaseq](https://github.com/nf-core/rnaseq) pipeline with a large dataset. This compute environment will also be used to run a Studios RStudio environment for interactive analysis of the resulting pipeline data. :::note The compute recommendations below are based on internal benchmarking performed by Seqera. See [RNA-Seq data and requirements](#rna-seq-data-and-requirements) for more information. @@ -51,7 +51,7 @@ The following compute resources are recommended for production RNA-Seq pipelines #### Fusion file system The [Fusion](../supported_software/fusion/fusion.mdx) file system enables seamless read and write operations to cloud object stores, leading to -simpler pipeline logic and faster, more efficient execution. While Fusion is not required to run nf-core/rnaseq, it is recommended for optimal performance. See [nf-core/rnaseq performance in Platform](#nf-corernaseq-performance-in-platform) at the end of this guide. +simpler pipeline logic and faster, more efficient execution. While Fusion is not required to run *nf-core/rnaseq*, it is recommended for optimal performance. See [nf-core/rnaseq performance in Platform](#nf-corernaseq-performance-in-platform) at the end of this guide. Fusion works best with AWS NVMe instances (fast instance storage) as this delivers the fastest performance when compared to environments using only AWS EBS (Elastic Block Store). Batch Forge selects instances automatically based on your compute environment configuration, but you can optionally specify instance types. To enable fast instance storage (see Create compute environment below), you must select EC2 instances with NVMe SSD storage (`m5d` or `r5d` families). @@ -95,7 +95,7 @@ The [nf-core/rnaseq](https://github.com/nf-core/rnaseq) pipeline is a highly con [Seqera Pipelines](https://seqera.io/pipelines) is a curated collection of quality open-source pipelines that can be imported directly to your workspace Launchpad in Platform. Each pipeline includes a dataset to use in a test run to confirm compute environment compatibility in just a few steps. -To use Seqera Pipelines to import the `nf-core/rnaseq` pipeline to your workspace: +To use Seqera Pipelines to import the *nf-core/rnaseq* pipeline to your workspace: ![Seqera Pipelines add to Launchpad](./_images/pipelines-add.gif) @@ -186,10 +186,10 @@ In Platform, samplesheets and other data can be made easily accessible in one of ## Launch pipeline :::note -This guide is based on version 3.15.1 of the nf-core/rnaseq pipeline. Launch form parameters and tools may differ in other versions. +This guide is based on version 3.15.1 of the *nf-core/rnaseq* pipeline. Launch form parameters and tools may differ in other versions. ::: -With your compute environment created, nf-core/rnaseq added to your workspace Launchpad, and your samplesheet accessible in Platform, you are ready to launch your pipeline. Navigate to the Launchpad and select **Launch** next to `nf-core-rnaseq` to open the launch form. +With your compute environment created, *nf-core/rnaseq* added to your workspace Launchpad, and your samplesheet accessible in Platform, you are ready to launch your pipeline. Navigate to the Launchpad and select **Launch** next to **nf-core-rnaseq** to open the launch form. The launch form consists of **General config**, **Run parameters**, and **Advanced options** sections to specify your run parameters before execution, and an execution summary. Use section headings or select the **Previous** and **Next** buttons at the bottom of the page to navigate between sections. @@ -276,7 +276,7 @@ After you have filled the necessary launch details, select **Launch**. The **Run ![Reports tab](./quickstart-demo/assets/reports-tab.png) - For example, for the nf-core/rnaseq pipeline, view the [MultiQC](https://docs.seqera.io/multiqc) report generated. MultiQC is a helpful reporting tool to generate aggregate statistics and summaries from bioinformatics tools. + For example, for the *nf-core/rnaseq* pipeline, view the [MultiQC](https://docs.seqera.io/multiqc) report generated. MultiQC is a helpful reporting tool to generate aggregate statistics and summaries from bioinformatics tools. ![Reports MultiQC preview](./quickstart-demo/assets/reports-preview.png) @@ -319,9 +319,9 @@ After you have filled the necessary launch details, select **Launch**. The **Run -## Interactive analysis with Data Studios +## Interactive analysis with Studios -**Data Studios** streamlines the process of creating interactive analysis environments for Platform users. With built-in templates for platforms like Jupyter Notebook, RStudio, and VSCode, creating a data studio is as simple as adding and sharing pipelines or datasets. The data studio URL can also be shared with any user with the [Connect role](../orgs-and-teams/roles.mdx) for real-time access and collaboration. +**Studios** streamline the process of creating interactive analysis environments for Platform users. With built-in templates for platforms like Jupyter Notebook, RStudio, and VSCode, creating a data studio is as simple as adding and sharing pipelines or datasets. The data studio URL can also be shared with any user with the [Connect role](../orgs-and-teams/roles.mdx) for real-time access and collaboration. For the purposes of this guide, an RStudio environment will be used to normalize the pipeline output data, perform differential expression analysis, and visualize the data with exploratory plots. @@ -329,11 +329,11 @@ For the purposes of this guide, an RStudio environment will be used to normalize #### Gene counts -Salmon is the default tool used during the `pseudo-aligner` step of the nf-core/rnaseq pipeline. In the pipeline output data, the `/salmon` directory contains the tool's output, including a `salmon.merged.gene_counts_length_scaled.tsv` file. +Salmon is the default tool used during the `pseudo-aligner` step of the *nf-core/rnaseq* pipeline. In the pipeline output data, the `/salmon` directory contains the tool's output, including a `salmon.merged.gene_counts_length_scaled.tsv` file. #### Sample info -The analysis script provided in this section requires a sample information file to parse the counts data in the `salmon.merged.gene_counts_length_scaled.tsv` file. nf-core/rnaseq does not produce this sample information file automatically. See below to create a sample information file based on the genes in your `salmon.merged.gene_counts_length_scaled.tsv` file. +The analysis script provided in this section requires a sample information file to parse the counts data in the `salmon.merged.gene_counts_length_scaled.tsv` file. *nf-core/rnaseq* does not produce this sample information file automatically. See below to create a sample information file based on the genes in your `salmon.merged.gene_counts_length_scaled.tsv` file.
**Create a sample info file** @@ -347,7 +347,7 @@ The analysis script provided in this section requires a sample information file - In the "Sample" column, write the exact sample name as it appears in the gene counts file. - In the "Group" column, write the corresponding group name. - For example, for the dataset used in a `test_full` run of nf-core/rnaseq, the `sampleinfo.txt` looks like this: + For example, for the dataset used in a `test_full` run of *nf-core/rnaseq*, the `sampleinfo.txt` looks like this: ``` Sample Group @@ -365,15 +365,15 @@ The analysis script provided in this section requires a sample information file
-### Create an RStudio analysis environment with Data Studios +### Create an RStudio analysis environment with Studios ![Add data studio](./_images/create-ds.gif) -From the **Data Studios** tab, select **Add a data studio** and complete the following: +From the **Studios** tab, select **Add a studio** and complete the following: - Select the latest **RStudio** container image template from the list. - Select your AWS Batch compute environment. :::note -Data studios compete for computing resources when sharing compute environments. Ensure your compute environment has sufficient resources to run both your pipelines and data studio sessions. The default CPU and memory allocation for a data studio is 2 CPUs and 8192 MB RAM. +Studio sessions compete for computing resources when sharing compute environments. Ensure your compute environment has sufficient resources to run both your pipelines and sessions. The default CPU and memory allocation for a Studio is 2 CPUs and 8192 MB RAM. ::: - Mount data using Data Explorer: Mount the S3 bucket or directory path that contains the pipeline work directory of your RNA-Seq run. - Optional: Enter CPU and memory allocations. The default values are 2 CPUs and 8192 MB memory (RAM). @@ -524,7 +524,7 @@ The RStudio environment can be configured with the packages you wish to install ``` :::info - This script is written for the analysis of human data, based on nf-core/rnaseq's `test_full` dataset. To adapt the script for your data, modify the contrasts based on the comparisons you want to make between your sample groups: + This script is written for the analysis of human data, based on *nf-core/rnaseq*'s `test_full` dataset. To adapt the script for your data, modify the contrasts based on the comparisons you want to make between your sample groups: ```r my.contrasts <- makeContrasts( @@ -656,11 +656,11 @@ RNA-Seq data typically consists of raw sequencing reads from high-throughput seq The compute recommendations in this guide are based on internal benchmarking performed by Seqera. Benchmark runs of [nf-core/rnaseq](https://github.com/nf-core/rnaseq) used profile `test_full`, consisting of an input dataset with 16 FASTQ files (8 paired-end samples) and a total size of approximately 123.5 GB. -This benchmark compares pipeline run metrics between single nf-core/rnaseq runs in an AWS Batch compute environment with Fusion file system and fast instance storage enabled (**Fusion** group) and an identical AWS Batch compute environment using S3 storage without Fusion (**AWS S3** group). +This benchmark compares pipeline run metrics between single *nf-core/rnaseq* runs in an AWS Batch compute environment with Fusion file system and fast instance storage enabled (**Fusion** group) and an identical AWS Batch compute environment using S3 storage without Fusion (**AWS S3** group). ### Pipeline steps and computing resource requirements -The nf-core/rnaseq pipeline involves several key steps, each with distinct computational requirements. Resource needs in this table are based on the `test_full` runs detailed previously: +The *nf-core/rnaseq* pipeline involves several key steps, each with distinct computational requirements. Resource needs in this table are based on the `test_full` runs detailed previously: | **Pipeline step** | **Tools** | **Resource needs** | **Description** | |-------------------------------------|---------------------------|------------------------------|---------------------------------------------------------------------------------------------------| @@ -686,7 +686,7 @@ The Fusion file system used with NVMe instance storage contributed to a 34% impr #### Process run time -The Fusion file system demonstrates significant performance improvements for most processes in the nf-core/rnaseq pipeline, particularly for I/O-intensive tasks: +The Fusion file system demonstrates significant performance improvements for most processes in the *nf-core/rnaseq* pipeline, particularly for I/O-intensive tasks: - The most time-consuming processes see improvements of 36.07% to 70.15%, saving hours of runtime in a full pipeline execution. - Most processes show significant performance improvements with Fusion, with time savings ranging from 35.57% to 99.14%. @@ -694,7 +694,7 @@ The Fusion file system demonstrates significant performance improvements for mos - SALMON_INDEX shows a notable 70.15% improvement, reducing runtime from 102.18 minutes to 30.50 minutes. - STAR_ALIGN_IGENOMES, one of the most time-consuming processes, is 53.82% faster with Fusion, saving nearly an hour of runtime. -![Average runtime of nf-core/rnaseq processes for eight samples using the Fusion file system and plain S3 storage. Error bars = standard deviation of the mean.](./_images/process-runtime-2.png) +![Average runtime of *nf-core/rnaseq* processes for eight samples using the Fusion file system and plain S3 storage. Error bars = standard deviation of the mean.](./_images/process-runtime-2.png) | Process | S3 Runtime (min) | Fusion Runtime (min) | Time Saved (min) | Improvement (%) | |---------|------------------|----------------------|------------------|-----------------| @@ -725,7 +725,7 @@ The Fusion file system demonstrates significant performance improvements for mos #### Optimize nf-core/rnaseq - Select the lightbulb icon next to nf-core/rnaseq in your workspace Launchpad to view the optimized profile. You have the flexibility to tailor the optimization's target settings and incorporate a retry strategy as needed. + Select the lightbulb icon next to *nf-core/rnaseq* in your workspace Launchpad to view the optimized profile. You have the flexibility to tailor the optimization's target settings and incorporate a retry strategy as needed. #### View optimized configuration diff --git a/platform_versioned_docs/version-24.3/getting-started/studios.mdx b/platform_versioned_docs/version-24.3/getting-started/studios.mdx index 4f5d9ff4d..aa0086e96 100644 --- a/platform_versioned_docs/version-24.3/getting-started/studios.mdx +++ b/platform_versioned_docs/version-24.3/getting-started/studios.mdx @@ -2,11 +2,11 @@ title: "Studios for interactive analysis" description: "Creating interactive analysis Studios for Jupyter, RStudio, VS Code, and more" date: "24 Feb 2025" -tags: [platform, studios, data studios, jupyter, rstudio, xpra, vscode, conda] +tags: [platform, studios, jupyter, rstudio, xpra, vscode, conda] toc_max_heading_level: 3 --- -[Studios](../data_studios/index.mdx) allows users to host a variety of container images directly in Seqera Platform compute environments for analysis using popular environments including [Jupyter](https://jupyter.org/) (Python) and [RStudio](https://posit.co/products/open-source/rstudio/) notebooks (R), [Visual Studio Code](https://code.visualstudio.com/) IDEs, and [Xpra](https://xpra.org/index.html) remote desktops. Each Studio session provides a dedicated interactive environment that encapsulates the live environment. +[Studios](../studios/index.mdx) allows users to host a variety of container images directly in Seqera Platform compute environments for analysis using popular environments including [Jupyter](https://jupyter.org/) (Python) and [RStudio](https://posit.co/products/open-source/rstudio/) notebooks (R), [Visual Studio Code](https://code.visualstudio.com/) IDEs, and [Xpra](https://xpra.org/index.html) remote desktops. Each Studio session provides a dedicated interactive environment that encapsulates the live environment. This guide explores how Studios integrates with your existing workflows, bridging the gap between pipeline execution and interactive analysis. It details how to set up and use each type of Studio, demonstrating a practical use case for each. @@ -430,7 +430,7 @@ The following R script installs and configures the prerequisite packages and lib devtools::install_github('pinin4fjords/shinyngs', upgrade_dependencies = FALSE) ``` - 1. Download the RDS file from nf-core AWS megatests or your own nf-core/differentialabundance results (see [Shiny app](https://nf-co.re/differentialabundance/1.5.0/docs/output/#shiny-app) from the nf-core documentation for file details): + 1. Download the RDS file from nf-core AWS megatests or your own *nf-core/differentialabundance* results (see [Shiny app](https://nf-co.re/differentialabundance/1.5.0/docs/output/#shiny-app) from the nf-core documentation for file details): ```r # For nf-core AWS megatests @@ -456,7 +456,7 @@ The following R script installs and configures the prerequisite packages and lib #### Interactive collaboration -To share a link to the running Studio session with collaborators inside your workspace, select the options menu for your RStudio session, then select **Copy Studio URL**. Using this link, other authenticated users can access the session directly to collaborate in real time. +To share a link to the running session with collaborators inside your workspace, select the options menu for your RStudio session, then select **Copy Studio URL**. Using this link, other authenticated users can access the session directly to collaborate in real time. ## Xpra: Visualize genetic variants with IGV @@ -510,8 +510,8 @@ From the **Studios** tab, select **Add a Studio** and complete the following: - igv - samtools ``` -- Select **Add** or choose to **Add and start** a Studio session immediately. -- If you chose to **Add** the Studio in the preceding step, select **Connect** in the options menu to open a Studio session in a new browser tab. +- Select **Add** or choose to **Add and start** a session immediately. +- If you chose to **Add** the Studio in the preceding step, select **Connect** in the options menu to open a session in a new browser tab. ### View variants in IGV desktop @@ -524,11 +524,11 @@ From the **Studios** tab, select **Add a Studio** and complete the following: #### Interactive collaboration -To share a link to the running Studio session with collaborators inside your workspace, select the options menu for your Xpra Studio session, then select **Copy Studio URL**. Using this link, other authenticated users can access the session directly to collaborate in real time. +To share a link to the running session with collaborators inside your workspace, select the options menu for your Xpra session, then select **Copy Studio URL**. Using this link, other authenticated users can access the session directly to collaborate in real time. ## VS Code: Create an interactive Nextflow development environment -Using Studios and Visual Studio Code allows you to create a portable and interactive Nextflow development environment with all the tools you need to develop and run Nextflow pipelines. This section demonstrates how to set up a VS Code Studio with Conda and nf-core tools, add public data and run the nf-core/fetchngs pipeline with the `test` profile, and create a VS Code project to start coding your own Nextflow pipelines. The Studio includes the [Nextflow VS Code extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow), which makes use of the Nextflow language server to provide syntax highlighting, code navigation, code completion, and diagnostics for Nextflow scripts and configuration files. +Using Studios and Visual Studio Code allows you to create a portable and interactive Nextflow development environment with all the tools you need to develop and run Nextflow pipelines. This section demonstrates how to set up a VS Code Studio with Conda and nf-core tools, add public data and run the *nf-core/fetchngs* pipeline with the `test` profile, and create a VS Code project to start coding your own Nextflow pipelines. The Studio includes the [Nextflow VS Code extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow), which makes use of the Nextflow language server to provide syntax highlighting, code navigation, code completion, and diagnostics for Nextflow scripts and configuration files. #### Create an AWS Batch compute environment @@ -600,4 +600,4 @@ nextflow run nf-core/fetchngs -profile test,conda --outdir ./nf-core-fetchngs-co #### Interactive collaboration -To share a link to the running Studio session with collaborators inside your workspace, select the options menu for your VS Code Studio session, then select **Copy Studio URL**. Using this link, other authenticated users can access the session directly to collaborate in real time. \ No newline at end of file +To share a link to the running session with collaborators inside your workspace, select the options menu for your VS Code Studio session, then select **Copy Studio URL**. Using this link, other authenticated users can access the session directly to collaborate in real time. \ No newline at end of file diff --git a/platform_versioned_docs/version-24.3/monitoring/configtables/log_events.yml b/platform_versioned_docs/version-24.3/monitoring/configtables/log_events.yml index 7b601e7d2..07557181d 100644 --- a/platform_versioned_docs/version-24.3/monitoring/configtables/log_events.yml +++ b/platform_versioned_docs/version-24.3/monitoring/configtables/log_events.yml @@ -16,11 +16,11 @@ Events logged: 'Add, edit, remove, hide, show' Note: 'Events for public and private buckets are logged.' - - Resource: 'Data Studios sessions' + Resource: 'Studios sessions' Events logged: 'Add, start, connect, disconnect, stop, delete' Note: 'Does not include temporary states (starting, stopping, deleting)' - - Resource: 'Data Studios custom environments' + Resource: 'Studios custom environments' Events logged: 'Build start, build success, build fail' Note: 'Applied only to Wave-enabled custom environment creation' - diff --git a/platform_versioned_docs/version-24.3/orgs-and-teams/roles.mdx b/platform_versioned_docs/version-24.3/orgs-and-teams/roles.mdx index f46ac5b78..41d68ccc0 100644 --- a/platform_versioned_docs/version-24.3/orgs-and-teams/roles.mdx +++ b/platform_versioned_docs/version-24.3/orgs-and-teams/roles.mdx @@ -20,10 +20,10 @@ You can group **members** and **collaborators** into **teams** and apply a role - **Owner**: The participant has full permissions for all resources within the workspace, including the workspace settings. - **Admin**: The participant has full permissions for resources associated with the workspace and access to all the actions associated with all roles, including all data-related roles. They can create, modify, and delete pipelines, compute environments, actions, credentials, and secrets. They can also add/remove users in the workspace and edit the workspace settings. A participant with this role cannot delete a workspace. -- **Maintain**: The participant can launch pipelines and modify pipeline executions (e.g., change the pipeline launch compute environment, parameters, pre/post-run scripts, Nextflow config), create new pipeline configurations in the Launchpad, and add secrets. They can upload, download, and preview data in Data Explorer, hide/unhide buckets, manage buckets, and manage the metadata associated with buckets.They can also add, update, and delete a data studio session. This includes starting, stopping, and changing the configuration. A participant with this role cannot modify compute environment settings and credentials, but can manage workspace labels and resource labels. -- **Launch**: The participant can launch pipelines and modify the pipeline input/output parameters in the Launchpad. This includes starting, stopping, and changing the configuration. They cannot modify the launch configuration or other resources. They can list, search and view the status, configuration, and details of data studio sessions and connect to a running data studio session. -- **Connect**: The participant can list, search, and view the status, configuration, and details of data studios sessions. They cannot add, update (start/stop/change config) or delete data studios sessions. They can also connect to a running data studio session and interact with the contents, and access team resources in read-only mode. They cannot launch or maintain pipelines. A participant with this role also cannot manage any data in Data Explorer — uploading, downloading, or previewing data, hiding/unhiding, managing buckets, or managing the metadata associated with buckets. -- **View**: The participant can only access team resources in read-only mode. This includes the ability to list, search, and view the status, configuration, and details of mounted data in Data Explorer and data studio sessions. +- **Maintain**: The participant can launch pipelines and modify pipeline executions (e.g., change the pipeline launch compute environment, parameters, pre/post-run scripts, Nextflow config), create new pipeline configurations in the Launchpad, and add secrets. They can upload, download, and preview data in Data Explorer, hide/unhide buckets, manage buckets, and manage the metadata associated with buckets.They can also add, update, and delete a Studio session. This includes starting, stopping, and changing the configuration. A participant with this role cannot modify compute environment settings and credentials, but can manage workspace labels and resource labels. +- **Launch**: The participant can launch pipelines and modify the pipeline input/output parameters in the Launchpad. This includes starting, stopping, and changing the configuration. They cannot modify the launch configuration or other resources. They can list, search and view the status, configuration, and details of Studio sessions and connect to a running session. +- **Connect**: The participant can list, search, and view the status, configuration, and details of Studio sessions. They cannot add, update (start/stop/change config) or delete Studio sessions. They can also connect to a running sessions and interact with the contents, and access team resources in read-only mode. They cannot launch or maintain pipelines. A participant with this role also cannot manage any data in Data Explorer — uploading, downloading, or previewing data, hiding/unhiding, managing buckets, or managing the metadata associated with buckets. +- **View**: The participant can only access team resources in read-only mode. This includes the ability to list, search, and view the status, configuration, and details of mounted data in Data Explorer and Studio sessions. ### Role inheritance diff --git a/platform_versioned_docs/version-24.3/studios/custom-envs.mdx b/platform_versioned_docs/version-24.3/studios/custom-envs.mdx index 900e39266..33b34413c 100644 --- a/platform_versioned_docs/version-24.3/studios/custom-envs.mdx +++ b/platform_versioned_docs/version-24.3/studios/custom-envs.mdx @@ -2,7 +2,7 @@ title: "Custom environments" description: "Custom environments for Studios" date: "1 Oct 2024" -tags: [environments, custom, studios] +tags: [environments, custom, studio, studio] --- In addition to the Seqera-provided container template images, you can provide your own custom container environments by augmenting the Seqera-provided images with a list of Conda packages or by providing your own base container template image. diff --git a/platform_versioned_docs/version-24.3/studios/index.mdx b/platform_versioned_docs/version-24.3/studios/index.mdx index 5e7ef41c6..652d3699c 100644 --- a/platform_versioned_docs/version-24.3/studios/index.mdx +++ b/platform_versioned_docs/version-24.3/studios/index.mdx @@ -28,7 +28,7 @@ Currently, Studios only supports AWS Batch compute environments that **do not** ## Limitations -If you configured your AWS Batch compute environment to include an EFS file system with **EFS file system > EFS mount path**, the mount path must be explicitly specified. The mount path cannot be the same as your compute environment work directory. If the EFS file system is mounted as your compute environment work directory, snapshots cannot be saved and sessions fail. To mount an EFS volume in a studio session (for example, if your organization has a custom, managed, and standardized software stack in an EFS volume), add the EFS volume to the compute environment (system ID and mount path). The volume will be available at the specified mount path in the session. +If you configured your AWS Batch compute environment to include an EFS file system with **EFS file system > EFS mount path**, the mount path must be explicitly specified. The mount path cannot be the same as your compute environment work directory. If the EFS file system is mounted as your compute environment work directory, snapshots cannot be saved and sessions fail. To mount an EFS volume in a Studio session (for example, if your organization has a custom, managed, and standardized software stack in an EFS volume), add the EFS volume to the compute environment (system ID and mount path). The volume will be available at the specified mount path in the session. For more information on AWS Batch configuration, see [AWS Batch][aws-batch]. @@ -115,17 +115,13 @@ To see the list of all Xpra image templates available, including security scan r Sessions have the following possible statuses: -- **building**: When a custom environment is building the template image for a new Studio session. The [Wave] service performs the build action. For more information on this status, see [Inspect custom container template build status][build-status]. +- **building**: When a custom environment is building the template image for a new session. The [Wave] service performs the build action. For more information on this status, see [Inspect custom container template build status][build-status]. - **build-failed**: When a custom environment build has failed. This is a non-recoverable error. Logs are provided to assist with troubleshooting. For more information on this status, see [Inspect custom container template build status][build-status]. - **starting**: The Studio is initializing. -- **running**: When a Studio session is **running**, you can connect to it, copy the URL, or stop it. In addition, the session can continue to process requests/run computations in the absence of an ongoing connection. -- **stopping**: The recently-running Studio session is in the process of being stopped. -- **stopped**: When a Studio session is stopped, the associated compute resources are deallocated. You can start or delete the session when it's in this state. -- **errored**: This state most often indicates that there has been an error starting the Studio session but it is in a **stopped** state. There might be errors reported by the session itself but these will be overwritten with a **running** status if the session is still running. - - :::tip - If you encounter an error with the public preview release of Studios, [contact Seqera support][contact]. - ::: +- **running**: When a session is **running**, you can connect to it, copy the URL, or stop it. In addition, the session can continue to process requests/run computations in the absence of an ongoing connection. +- **stopping**: The recently-running session is in the process of being stopped. +- **stopped**: When a session is stopped, the associated compute resources are deallocated. You can start or delete the session when it's in this state. +- **errored**: This state most often indicates that there has been an error starting the session but it is in a **stopped** state. There might be errors reported by the session itself but these will be overwritten with a **running** status if the session is still running. ## Studio session data links @@ -144,9 +140,9 @@ For more information, see [Limit Studio access to a specific cloud bucket subdir ## Studio session checkpoints -When starting a Studio session, a *checkpoint* is automatically created. A checkpoint saves all changes made to the root filesystem and stores it in the attached compute environment's pipeline work directory in the `.studios/checkpoints` folder with a unique name. The current checkpoint is updated every five minutes during a session. +When starting a session, a *checkpoint* is automatically created. A checkpoint saves all changes made to the root filesystem and stores it in the attached compute environment's pipeline work directory in the `.studios/checkpoints` folder with a unique name. The current checkpoint is updated every five minutes during a session. -When you stop and start a Studios session, or start a new session from a previously created checkpoint, changes such as installed software packages and configuration files are restored and made available. Changes made to mounted data are not included in a checkpoint. +When you stop and start a session, or start a new session from a previously created checkpoint, changes such as installed software packages and configuration files are restored and made available. Changes made to mounted data are not included in a checkpoint. Checkpoints can be renamed and the name has to be unique per Studio. Spaces in checkpoint names are converted to underscores automatically. diff --git a/platform_versioned_docs/version-24.3/studios/managing.mdx b/platform_versioned_docs/version-24.3/studios/managing.mdx index 2bdaf86f6..4823ed0c9 100644 --- a/platform_versioned_docs/version-24.3/studios/managing.mdx +++ b/platform_versioned_docs/version-24.3/studios/managing.mdx @@ -118,7 +118,7 @@ To share a link to a running session with collaborators inside your workspace, s Collaborators need valid workspace permissions to connect to the running Studio. ::: -## Stop a Studio +## Stop a Studio session This functionality is available to users with the **Maintain** role and above. @@ -126,19 +126,17 @@ To stop a running session, select the three dots next to the status message and Stopping a running session creates a new checkpoint. -## Restart a stopped Studio +## Restart a stopped session -This functionality is available to users with the **Maintain** role and above. - -When you restart a stopped session, the session uses the most recent checkpoint. +This functionality is available to users with the **Maintain** role and above. When you restart a stopped session, the session uses the most recent checkpoint. ## Start a new session from a checkpoint This functionality is available to users with the **Maintain** role and above. -You can start a new session from an existing stopped session. This will inherit the history of the parent checkpoint state. From the list of **stopped** Studios in your workspace, select the three dots next to the status message for the data studio and select **Start as new**. Alternatively, select the **Checkpoints** tab on the detail page, select the three dots in the **Actions** column, and then select **Start as new** to start a new session. +You can start a new session from an existing stopped session. This will inherit the history of the parent checkpoint state. From the list of **stopped** Studios in your workspace, select the three dots next to the status message for the Studio you want to start and select **Start as new**. Alternatively, select the **Checkpoints** tab on the detail page, select the three dots in the **Actions** column, and then select **Start as new** to start a new session. -## Delete a Studio session +## Delete a Studios This functionality is available to users with the **Maintain** role and above. @@ -160,7 +158,7 @@ To limit read-write access to a specific subdirectory, complete the following st - Optional: **Description**: Enter a description for this cloud bucket. 1. Select **Add** to create a custom data-link to a subdirectory in the cloud bucket. -When defining a new Studio session, you can configure the **Mounted data** by selecting the custom data-link created by the previous steps. +When defining a new Studio, you can configure the **Mounted data** by selecting the custom data-link created by the previous steps. {/* links */} diff --git a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx index f56e0bf18..75cbf93a7 100644 --- a/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx +++ b/platform_versioned_docs/version-24.3/troubleshooting_and_faqs/studios_troubleshooting.mdx @@ -2,44 +2,46 @@ title: "Studios" description: "Studios troubleshooting with Seqera Platform." date: "26 August 2024" -tags: [faq, help, data studios, troubleshooting] +tags: [faq, help, studios, troubleshooting] --- ## View all mounted datasets -In your interactive analysis environment, open a new terminal and type `ls -la /workspace/data`. This displays all the mounted datasets available in the current studio session. +In your interactive analysis environment, open a new terminal and type `ls -la /workspace/data`. This displays all the mounted datasets available in the current session. ![](./_images/studios_notebook_fusion.png) -## Studio session is stuck in **starting** +## Session is stuck in **starting** -If your studio session doesn't advance from **starting** status to **running** status within 30 minutes, and you have access to the AWS Console for your organization, check that the AWS Batch compute environment associated with the Studio session is in the **ENABLED** state with a **VALID** status. You can also check the **Compute resources** settings. Contact your organization's AWS administrator if you don't have access to the AWS Console. +If your Studio session doesn't advance from **starting** status to **running** status within 30 minutes, and you have access to the AWS Console for your organization, check that the AWS Batch compute environment associated with the session is in the **ENABLED** state with a **VALID** status. You can also check the **Compute resources** settings. Contact your organization's AWS administrator if you don't have access to the AWS Console. If sufficient compute environment resources are unavailable, **Stop** the session and any others that may be running before trying again. If you have access to the AWS Console for your organization, you can terminate a specific session from the AWS Batch Jobs page (filtering by compute environment queue). -## Studio session status is **errored** +## Session status is **errored** -The **errored** status is generally related to issues encountered when creating the studio session resources in the compute environment (e.g., invalid credentials, insufficient permissions, network issues). It can also be related to insufficient compute resources, which are set in your compute environment configuration. Contact your organization's AWS administrator if you don't have access to the AWS Console. Also contact your Seqera account executive so we can investigate the issue. +The **errored** status is generally related to issues encountered when creating the Studio session resources in the compute environment (e.g., invalid credentials, insufficient permissions, network issues). It can also be related to insufficient compute resources, which are set in your compute environment configuration. Contact your organization's AWS administrator if you don't have access to the AWS Console. Also contact your Seqera account executive so we can investigate the issue. -## Studio session can't be **stopped** +## Session can't be **stopped** If you're not able to stop a session, it's usually because the Batch job running the session failed for some reason. In this case, and if you have access to the AWS Console for your organization, you can stop the session from the compute environment screen. Contact your organization's AWS administrator if you don't have access to the AWS Console. Also contact your Seqera account executive so we can investigate the issue. -## Studio session performance is poor +## Session performance is poor -A slow or unresponsive Studio session may be due to its AWS Batch compute environment being utilized for other jobs, such as running Nextflow pipelines. The compute environment is responsible for scheduling jobs to the available compute resources. Studio sessions compete for resources with the Nextflow pipeline head job and Seqera does not currently have an established pattern of precedence. +A slow or unresponsive session may be due to its AWS Batch compute environment being utilized for other jobs, such as running Nextflow pipelines. The compute environment is responsible for scheduling jobs to the available compute resources. Sessions compete for resources with the Nextflow pipeline head job and Seqera does not currently have an established pattern of precedence. If you have access to the AWS Console for your organization, check the jobs associated with the AWS Batch compute environment and compare the resources allocated with its **Compute resources** settings. -## Memory allocation of the Studio session is exceeded +## Memory allocation of the session is exceeded -The running container in the AWS Batch compute environment inherits the memory limits specified by the session configuration when adding or starting the session. The kernel then handles the memory as if running natively on Linux. Linux can overcommit memory, leading to possible out-of-memory errors in a container environment. The kernel has protections in place to prevent this, but it can happen, and in this case, the process is killed. This can manifest as a performance lag, killed subprocesses, or at worst, a killed session. Running sessions have automated snapshots created every five minutes, so if the running container is killed only those changes made after the prior snapshot creation will be lost. +The running container in the AWS Batch compute environment inherits the memory limits specified by the session configuration when adding or starting the session. The kernel then handles the memory as if running natively on Linux. Linux can overcommit memory, leading to possible out-of-memory errors in a container environment. The kernel has protections in place to prevent this, but it can happen, and in this case, the process is killed. This can manifest as a performance lag, killed subprocesses, or at worst, a killed session. + +Running sessions have automated snapshots created every five minutes, so if the running container is killed only those changes made after the prior snapshot creation will be lost. ## All datasets are read-only By default, AWS Batch compute environments that are created with Batch Forge restrict access to S3 to the working directory only, unless additional **Allowed S3 Buckets** are specified. If the compute environment does not have write access to the mounted dataset, it will be mounted as read-only. -## My Studio session with GPU isn't starting +## My session with GPU isn't starting Check whether the instance type you selected [supports GPU](https://aws.amazon.com/ec2/instance-types/). If you specify multiple GPUs make sure that multi-GPU instances can be launched by your compute environment and are not limited by the maximum CPU config that you've set. From 58430b1a80cdb08cfe2eaa2a6b3aa43d6c668fcf Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 25 Feb 2025 22:37:49 +0200 Subject: [PATCH 28/30] Fixed broken internal links --- .../version-24.2/enterprise/docker-compose.mdx | 2 +- platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx b/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx index 714bf3e4d..ce940c311 100644 --- a/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx @@ -45,7 +45,7 @@ For more information on configuration, see [Configuration options](./configurati ### Studios -[Studios](../studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](./studios.mdx). +[Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](./studios.mdx). :::note Studios is currently in **public preview** and is available from Seqera Platform v24.1. If you experience any problems during the deployment process please contact your account executive. Data Studios in Enterprise is not installed by default. diff --git a/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx b/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx index b5b0fe62b..44bf55e75 100644 --- a/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx @@ -252,7 +252,7 @@ The initContainers will wait until both the Seqera and pipeline optimization ser ### Studios -[Studios](../studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](./studios.mdx). +[Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](./data_studios.mdx). :::note Studios is currently in **public preview** and is available from Seqera Platform v24.1. If you experience any problems during the deployment process [contact Seqera support](https://support.seqera.io). Studios in Enterprise is not installed by default. From 962abb9efdfa087be1275ba7475ae9f5a4ed51f8 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 25 Feb 2025 22:44:15 +0200 Subject: [PATCH 29/30] broken link --- .../version-24.2/enterprise/docker-compose.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx b/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx index ce940c311..6da7f3a6f 100644 --- a/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/docker-compose.mdx @@ -45,7 +45,7 @@ For more information on configuration, see [Configuration options](./configurati ### Studios -[Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](./studios.mdx). +[Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](../enterprise/studios.mdx). :::note Studios is currently in **public preview** and is available from Seqera Platform v24.1. If you experience any problems during the deployment process please contact your account executive. Data Studios in Enterprise is not installed by default. From 37e562d31f12b379173c5408ee9b4e94460e905a Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 25 Feb 2025 23:00:34 +0200 Subject: [PATCH 30/30] Broken link --- platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx b/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx index 44bf55e75..c48ea4de6 100644 --- a/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx +++ b/platform_versioned_docs/version-24.2/enterprise/kubernetes.mdx @@ -252,7 +252,7 @@ The initContainers will wait until both the Seqera and pipeline optimization ser ### Studios -[Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](./data_studios.mdx). +[Studios](../data_studios/index.mdx) is an interactive analysis environment available in organizational workspaces. To enable Studios, see [Studios deployment](./studios.mdx). :::note Studios is currently in **public preview** and is available from Seqera Platform v24.1. If you experience any problems during the deployment process [contact Seqera support](https://support.seqera.io). Studios in Enterprise is not installed by default.