From 4c9eb45f5bf5f9a3bbfd22f80bda77fdc7f1dca8 Mon Sep 17 00:00:00 2001 From: nbokulich Date: Wed, 5 Jun 2024 08:49:44 +0200 Subject: [PATCH 1/4] rename shotgun->metagenome and update plugin list --- source/glossary.rst | 2 +- source/install/index.rst | 14 ++++++++---- source/install/native.rst | 48 +++++++++++++++++++-------------------- 3 files changed, 34 insertions(+), 30 deletions(-) diff --git a/source/glossary.rst b/source/glossary.rst index 5d52eee9..9dc17eec 100644 --- a/source/glossary.rst +++ b/source/glossary.rst @@ -63,7 +63,7 @@ and another geared toward developers. You can find the A collection of QIIME 2 plugins that are designed to be installed together. These are generally grouped by a theme. For example, the Amplicon Distribution provides a collection of plugins for analysis of - microbiome amplicon data, while the Shotgun Distribution provides a + microbiome amplicon data, while the Metagenome Distribution provides a collection of plugins for analysis of microbiome shotgun metagenomics data. diff --git a/source/install/index.rst b/source/install/index.rst index f2350761..b710cba3 100644 --- a/source/install/index.rst +++ b/source/install/index.rst @@ -44,7 +44,7 @@ QIIME 2 2024.10 distributions As of 2024.10, QIIME 2 releases now include the following QIIME 2 distributions that are available for install: - ``amplicon`` -- ``shotgun`` +- ``metagenome`` - ``tiny`` QIIME 2 2024.10 Amplicon Distribution @@ -73,13 +73,15 @@ The 2024.10 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 fr - ``q2-taxa`` - ``q2-types`` - ``q2-vsearch`` +- ``rescript`` -QIIME 2 2024.10 Shotgun Distribution +QIIME 2 2024.10 Metagenome Distribution .................................... -The 2024.10 release of the QIIME 2 Shotgun Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins: +The 2024.10 release of the QIIME 2 Metagenome Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins: - ``q2-assembly`` +- ``q2-composition`` - ``q2-cutadapt`` - ``q2-demux`` - ``q2-diversity`` @@ -87,6 +89,8 @@ The 2024.10 release of the QIIME 2 Shotgun Distribution includes the QIIME 2 fra - ``q2-emperor`` - ``q2-feature-classifier`` - ``q2-feature-table`` +- ``q2-fondue`` +- ``q2-longitudinal`` - ``q2-metadata`` - ``q2-moshpit`` - ``q2-quality-control`` @@ -95,7 +99,7 @@ The 2024.10 release of the QIIME 2 Shotgun Distribution includes the QIIME 2 fra - ``q2-sapienns`` - ``q2-taxa`` - ``q2-types`` -- ``q2-types-genomics`` +- ``q2-vsearch`` - ``rescript`` QIIME 2 2024.10 Tiny Distribution @@ -105,7 +109,7 @@ The 2024.10 release of the QIIME 2 Tiny Distribution includes the QIIME 2 framew - ``q2-types`` -The QIIME 2 Tiny Distribution is a minimal QIIME 2 environment that can be used by developers who are in need of a basic development environment, or community plugin users who do not need the entire Amplicon or Shotgun Distributions in their QIIME 2 environment. +The QIIME 2 Tiny Distribution is a minimal QIIME 2 environment that can be used by developers who are in need of a basic development environment, or community plugin users who do not need the entire Amplicon or Metagenome Distributions in their QIIME 2 environment. .. note:: The Amplicon Distribution is necessary to run the commands in the :doc:`QIIME 2 tutorials <../tutorials/index>`. If there are additional QIIME 2 plugins or interfaces you would like to install, please consult the relevant package(s) documentation. diff --git a/source/install/native.rst b/source/install/native.rst index ba528a80..1132b35a 100644 --- a/source/install/native.rst +++ b/source/install/native.rst @@ -100,52 +100,52 @@ QIIME 2 Amplicon Distribution -QIIME 2 Shotgun Distribution +QIIME 2 Metagenome Distribution ............................ .. raw:: html
-
+

From the above tabs, please choose the installation instructions that are appropriate for your platform.

-
- 
wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.10-py38-osx-conda.yml
-   conda env create -n qiime2-shotgun-2024.10 --file qiime2-shotgun-2024.10-py38-osx-conda.yml
+
+ 
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py38-osx-conda.yml
+   conda env create -n qiime2-metagenome-2024.10 --file qiime2-metagenome-2024.10-py38-osx-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-shotgun-2024.10-py38-osx-conda.yml
+ 
rm qiime2-metagenome-2024.10-py38-osx-conda.yml
-
+

These instructions are for users with Apple Silicon chips (M1, M2, etc), and configures the installation of QIIME 2 in Rosetta 2 emulation mode.

- 
wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.10-py38-osx-conda.yml
-   CONDA_SUBDIR=osx-64 conda env create -n qiime2-shotgun-2024.10 --file qiime2-shotgun-2024.10-py38-osx-conda.yml
-   conda activate qiime2-shotgun-2024.10
+            
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py38-osx-conda.yml
+   CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2024.10 --file qiime2-metagenome-2024.10-py38-osx-conda.yml
+   conda activate qiime2-metagenome-2024.10
    conda config --env --set subdir osx-64

    OPTIONAL CLEANUP
-   
rm qiime2-shotgun-2024.10-py38-osx-conda.yml

+   
rm qiime2-metagenome-2024.10-py38-osx-conda.yml
-
- 
wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-shotgun-2024.10 --file qiime2-shotgun-2024.10-py38-linux-conda.yml
+
+ 
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py38-linux-conda.yml
+   conda env create -n qiime2-metagenome-2024.10 --file qiime2-metagenome-2024.10-py38-linux-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-shotgun-2024.10-py38-linux-conda.yml
+ 
rm qiime2-metagenome-2024.10-py38-linux-conda.yml
-
+

These instructions are identical to the Linux instructions and are intended for users of the Windows Subsystem for Linux.

- 
wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-shotgun-2024.10 --file qiime2-shotgun-2024.10-py38-linux-conda.yml
+ 
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py38-linux-conda.yml
+   conda env create -n qiime2-metagenome-2024.10 --file qiime2-metagenome-2024.10-py38-linux-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-shotgun-2024.10-py38-linux-conda.yml
+ 
rm qiime2-metagenome-2024.10-py38-linux-conda.yml
From 6f41146077693ba0e92a6ccd453a9d9ef5e69f7e Mon Sep 17 00:00:00 2001 From: Liz Gehret Date: Wed, 5 Jun 2024 10:30:38 -0700 Subject: [PATCH 2/4] fix syntax --- source/install/native.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/install/native.rst b/source/install/native.rst index 1132b35a..a8927f58 100644 --- a/source/install/native.rst +++ b/source/install/native.rst @@ -101,7 +101,7 @@ QIIME 2 Amplicon Distribution
QIIME 2 Metagenome Distribution -............................ +............................... .. raw:: html From 40d39a1a64693a9e5e3b54d551ebf0c72e5752db Mon Sep 17 00:00:00 2001 From: Liz Gehret Date: Wed, 5 Jun 2024 10:35:02 -0700 Subject: [PATCH 3/4] revert 2024.10 -> 2024.5 --- source/data-resources.rst | 12 +-- source/install/index.rst | 24 ++--- source/install/native.rst | 90 +++++++++---------- source/install/virtual/docker.rst | 4 +- source/tutorials/atacama-soils.rst | 10 +-- source/tutorials/chimera.rst | 4 +- source/tutorials/exporting.rst | 4 +- source/tutorials/feature-classifier.rst | 6 +- source/tutorials/filtering.rst | 10 +-- source/tutorials/fmt.rst | 12 +-- source/tutorials/importing.rst | 38 ++++---- source/tutorials/longitudinal.rst | 10 +-- source/tutorials/metadata.rst | 16 ++-- source/tutorials/moving-pictures-usage.rst | 8 +- source/tutorials/moving-pictures.rst | 10 +-- source/tutorials/otu-clustering.rst | 4 +- source/tutorials/overview.rst | 4 +- source/tutorials/pd-mice.rst | 18 ++-- source/tutorials/phylogeny.rst | 2 +- ...for-experienced-microbiome-researchers.rst | 2 +- source/tutorials/quality-control.rst | 10 +-- source/tutorials/read-joining.rst | 4 +- source/tutorials/sample-classifier.rst | 8 +- source/tutorials/utilities.rst | 10 +-- 24 files changed, 160 insertions(+), 160 deletions(-) diff --git a/source/data-resources.rst b/source/data-resources.rst index df5bb267..0faeacaa 100644 --- a/source/data-resources.rst +++ b/source/data-resources.rst @@ -33,10 +33,10 @@ QIIME-compatible SILVA releases (up to release 132), as well as the licensing in We also provide pre-formatted SILVA reference sequence and taxonomy files here that were processed using `RESCRIPt `_. See licensing information below if you use these files. -- `Silva 138 SSURef NR99 full-length sequences `_ (MD5: ``de8886bb2c059b1e8752255d271f3010``) -- `Silva 138 SSURef NR99 full-length taxonomy `_ (MD5: ``f12d5b78bf4b1519721fe52803581c3d``) -- `Silva 138 SSURef NR99 515F/806R region sequences `_ (MD5: ``a914837bc3f8964b156a9653e2420d22``) -- `Silva 138 SSURef NR99 515F/806R region taxonomy `_ (MD5: ``e2c40ae4c60cbf75e24312bb24652f2c``) +- `Silva 138 SSURef NR99 full-length sequences `_ (MD5: ``de8886bb2c059b1e8752255d271f3010``) +- `Silva 138 SSURef NR99 full-length taxonomy `_ (MD5: ``f12d5b78bf4b1519721fe52803581c3d``) +- `Silva 138 SSURef NR99 515F/806R region sequences `_ (MD5: ``a914837bc3f8964b156a9653e2420d22``) +- `Silva 138 SSURef NR99 515F/806R region taxonomy `_ (MD5: ``e2c40ae4c60cbf75e24312bb24652f2c``) Please cite the following references if you use any of these pre-formatted files: @@ -79,5 +79,5 @@ The following databases are intended for use with q2-fragment-insertion, and are constructed directly from the `SEPP-Refs project `_. -- `Silva 128 SEPP reference database `_ (MD5: ``7879792a6f42c5325531de9866f5c4de``) -- `Greengenes 13_8 SEPP reference database `_ (MD5: ``9ed215415b52c362e25cb0a8a46e1076``) +- `Silva 128 SEPP reference database `_ (MD5: ``7879792a6f42c5325531de9866f5c4de``) +- `Greengenes 13_8 SEPP reference database `_ (MD5: ``9ed215415b52c362e25cb0a8a46e1076``) diff --git a/source/install/index.rst b/source/install/index.rst index b710cba3..08718e44 100644 --- a/source/install/index.rst +++ b/source/install/index.rst @@ -38,19 +38,19 @@ option for all cases. In general we recommend the following: .. _distributions: -QIIME 2 2024.10 distributions ------------------------------ +QIIME 2 2024.5 distributions +---------------------------- -As of 2024.10, QIIME 2 releases now include the following QIIME 2 distributions that are available for install: +As of 2024.5, QIIME 2 releases now include the following QIIME 2 distributions that are available for install: - ``amplicon`` - ``metagenome`` - ``tiny`` -QIIME 2 2024.10 Amplicon Distribution -..................................... +QIIME 2 2024.5 Amplicon Distribution +.................................... -The 2024.10 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins: +The 2024.5 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins: - ``q2-alignment`` - ``q2-composition`` @@ -75,10 +75,10 @@ The 2024.10 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 fr - ``q2-vsearch`` - ``rescript`` -QIIME 2 2024.10 Metagenome Distribution -.................................... +QIIME 2 2024.5 Metagenome Distribution +...................................... -The 2024.10 release of the QIIME 2 Metagenome Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins: +The 2024.5 release of the QIIME 2 Metagenome Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins: - ``q2-assembly`` - ``q2-composition`` @@ -102,10 +102,10 @@ The 2024.10 release of the QIIME 2 Metagenome Distribution includes the QIIME 2 - ``q2-vsearch`` - ``rescript`` -QIIME 2 2024.10 Tiny Distribution -................................. +QIIME 2 2024.5 Tiny Distribution +................................ -The 2024.10 release of the QIIME 2 Tiny Distribution includes the QIIME 2 framework and ``q2cli`` (a QIIME 2 command-line interface) and the following plugins: +The 2024.5 release of the QIIME 2 Tiny Distribution includes the QIIME 2 framework and ``q2cli`` (a QIIME 2 command-line interface) and the following plugins: - ``q2-types`` diff --git a/source/install/native.rst b/source/install/native.rst index a8927f58..dfc45b52 100644 --- a/source/install/native.rst +++ b/source/install/native.rst @@ -42,13 +42,13 @@ Install QIIME 2 within a ``conda`` environment ---------------------------------------------- Once you have Miniconda installed, create a ``conda`` environment and install -the QIIME 2 2024.10 distribution of your choice within the environment. +the QIIME 2 2024.5 distribution of your choice within the environment. We **highly** recommend creating a *new* environment specifically for the QIIME 2 distribution and release being installed, as there are many required dependencies that you may not want added to an existing environment. You can choose whatever name you'd like for the environment. -In this example, we'll name the environments ``qiime2--2024.10`` -to indicate what QIIME 2 release is installed (i.e. ``2024.10``). +In this example, we'll name the environments ``qiime2--2024.5`` +to indicate what QIIME 2 release is installed (i.e. ``2024.5``). QIIME 2 Amplicon Distribution ............................. @@ -70,32 +70,32 @@ QIIME 2 Amplicon Distribution

- 
wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py38-osx-conda.yml
-   conda env create -n qiime2-amplicon-2024.10 --file qiime2-amplicon-2024.10-py38-osx-conda.yml
+ 
wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py38-osx-conda.yml
+   conda env create -n qiime2-amplicon-2024.5 --file qiime2-amplicon-2024.5-py38-osx-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-amplicon-2024.10-py38-osx-conda.yml
+ 
rm qiime2-amplicon-2024.5-py38-osx-conda.yml

These instructions are for users with Apple Silicon chips (M1, M2, etc), and configures the installation of QIIME 2 in Rosetta 2 emulation mode.

- 
wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py38-osx-conda.yml
-   CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.10 --file qiime2-amplicon-2024.10-py38-osx-conda.yml
-   conda activate qiime2-amplicon-2024.10
+            
wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py38-osx-conda.yml
+   CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.5 --file qiime2-amplicon-2024.5-py38-osx-conda.yml
+   conda activate qiime2-amplicon-2024.5
    conda config --env --set subdir osx-64

    OPTIONAL CLEANUP
-   
rm qiime2-amplicon-2024.10-py38-osx-conda.yml

+   
rm qiime2-amplicon-2024.5-py38-osx-conda.yml
- 
wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-amplicon-2024.10 --file qiime2-amplicon-2024.10-py38-linux-conda.yml
+ 
wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-amplicon-2024.5 --file qiime2-amplicon-2024.5-py38-linux-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-amplicon-2024.10-py38-linux-conda.yml
+ 
rm qiime2-amplicon-2024.5-py38-linux-conda.yml

These instructions are identical to the Linux instructions and are intended for users of the Windows Subsystem for Linux.

- 
wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-amplicon-2024.10 --file qiime2-amplicon-2024.10-py38-linux-conda.yml
+ 
wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-amplicon-2024.5 --file qiime2-amplicon-2024.5-py38-linux-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-amplicon-2024.10-py38-linux-conda.yml
+ 
rm qiime2-amplicon-2024.5-py38-linux-conda.yml
@@ -120,32 +120,32 @@ QIIME 2 Metagenome Distribution

- 
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py38-osx-conda.yml
-   conda env create -n qiime2-metagenome-2024.10 --file qiime2-metagenome-2024.10-py38-osx-conda.yml
+ 
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py38-osx-conda.yml
+   conda env create -n qiime2-metagenome-2024.5 --file qiime2-metagenome-2024.5-py38-osx-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-metagenome-2024.10-py38-osx-conda.yml
+ 
rm qiime2-metagenome-2024.5-py38-osx-conda.yml

These instructions are for users with Apple Silicon chips (M1, M2, etc), and configures the installation of QIIME 2 in Rosetta 2 emulation mode.

- 
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py38-osx-conda.yml
-   CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2024.10 --file qiime2-metagenome-2024.10-py38-osx-conda.yml
-   conda activate qiime2-metagenome-2024.10
+            
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py38-osx-conda.yml
+   CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2024.5 --file qiime2-metagenome-2024.5-py38-osx-conda.yml
+   conda activate qiime2-metagenome-2024.5
    conda config --env --set subdir osx-64

    OPTIONAL CLEANUP
-   
rm qiime2-metagenome-2024.10-py38-osx-conda.yml

+   
rm qiime2-metagenome-2024.5-py38-osx-conda.yml
- 
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-metagenome-2024.10 --file qiime2-metagenome-2024.10-py38-linux-conda.yml
+ 
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-metagenome-2024.5 --file qiime2-metagenome-2024.5-py38-linux-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-metagenome-2024.10-py38-linux-conda.yml
+ 
rm qiime2-metagenome-2024.5-py38-linux-conda.yml

These instructions are identical to the Linux instructions and are intended for users of the Windows Subsystem for Linux.

- 
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-metagenome-2024.10 --file qiime2-metagenome-2024.10-py38-linux-conda.yml
+ 
wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-metagenome-2024.5 --file qiime2-metagenome-2024.5-py38-linux-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-metagenome-2024.10-py38-linux-conda.yml
+ 
rm qiime2-metagenome-2024.5-py38-linux-conda.yml
@@ -170,32 +170,32 @@ QIIME 2 Tiny Distribution

- 
wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py38-osx-conda.yml
-   conda env create -n qiime2-tiny-2024.10 --file qiime2-tiny-2024.10-py38-osx-conda.yml
+ 
wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py38-osx-conda.yml
+   conda env create -n qiime2-tiny-2024.5 --file qiime2-tiny-2024.5-py38-osx-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-tiny-2024.10-py38-osx-conda.yml
+ 
rm qiime2-tiny-2024.5-py38-osx-conda.yml

These instructions are for users with Apple Silicon chips (M1, M2, etc), and configures the installation of QIIME 2 in Rosetta 2 emulation mode.

- 
wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py38-osx-conda.yml
-   CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2024.10 --file qiime2-tiny-2024.10-py38-osx-conda.yml
-   conda activate qiime2-tiny-2024.10
+            
wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py38-osx-conda.yml
+   CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2024.5 --file qiime2-tiny-2024.5-py38-osx-conda.yml
+   conda activate qiime2-tiny-2024.5
    conda config --env --set subdir osx-64

    OPTIONAL CLEANUP
-   
rm qiime2-tiny-2024.10-py38-osx-conda.yml

+   
rm qiime2-tiny-2024.5-py38-osx-conda.yml
- 
wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-tiny-2024.10 --file qiime2-tiny-2024.10-py38-linux-conda.yml
+ 
wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-tiny-2024.5 --file qiime2-tiny-2024.5-py38-linux-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-tiny-2024.10-py38-linux-conda.yml
+ 
rm qiime2-tiny-2024.5-py38-linux-conda.yml

These instructions are identical to the Linux instructions and are intended for users of the Windows Subsystem for Linux.

- 
wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-tiny-2024.10 --file qiime2-tiny-2024.10-py38-linux-conda.yml
+ 
wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-tiny-2024.5 --file qiime2-tiny-2024.5-py38-linux-conda.yml
OPTIONAL CLEANUP - 
rm qiime2-tiny-2024.10-py38-linux-conda.yml
+ 
rm qiime2-tiny-2024.5-py38-linux-conda.yml
@@ -208,7 +208,7 @@ Now that you have a QIIME 2 environment, activate it using the environment's nam .. command-block:: :no-exec: - conda activate qiime2--2024.10 + conda activate qiime2--2024.5 To deactivate an environment, run ``conda deactivate``. @@ -247,13 +247,13 @@ of QIIME 2 and one with the newer version. ----------------------- If at any point during the analysis the QIIME 2 conda environment is closed -or deactivated, QIIME 2 2024.10 can be activated (or reactivated) by running +or deactivated, QIIME 2 2024.5 can be activated (or reactivated) by running the following command: .. command-block:: :no-exec: - conda activate qiime2--2024.10 + conda activate qiime2--2024.5 To determine the currently active conda environment, run the following command and look for the line that starts with "active environment": diff --git a/source/install/virtual/docker.rst b/source/install/virtual/docker.rst index 299e287b..799bc5bf 100644 --- a/source/install/virtual/docker.rst +++ b/source/install/virtual/docker.rst @@ -14,7 +14,7 @@ In a terminal with Docker activated, run: .. command-block:: :no-exec: - docker pull quay.io/qiime2/amplicon:2024.10 + docker pull quay.io/qiime2/amplicon:2024.5 3. Confirm the installation --------------------------- @@ -24,4 +24,4 @@ Run the following to confirm that the image was successfully fetched. .. command-block:: :no-exec: - docker run -t -i -v $(pwd):/data quay.io/qiime2/amplicon:2024.10 qiime + docker run -t -i -v $(pwd):/data quay.io/qiime2/amplicon:2024.5 qiime diff --git a/source/tutorials/atacama-soils.rst b/source/tutorials/atacama-soils.rst index 3ad7aad3..8c72aafc 100644 --- a/source/tutorials/atacama-soils.rst +++ b/source/tutorials/atacama-soils.rst @@ -45,7 +45,7 @@ available as a Google Sheet. This ``sample-metadata.tsv`` file is used throughout the rest of the tutorial. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/sample_metadata.tsv + :url: https://data.qiime2.org/2024.5/tutorials/atacama-soils/sample_metadata.tsv :saveas: sample-metadata.tsv @@ -61,15 +61,15 @@ tutorial to further improve the run time. mkdir emp-paired-end-sequences .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/10p/forward.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/atacama-soils/10p/forward.fastq.gz :saveas: emp-paired-end-sequences/forward.fastq.gz .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/10p/reverse.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/atacama-soils/10p/reverse.fastq.gz :saveas: emp-paired-end-sequences/reverse.fastq.gz .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/10p/barcodes.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/atacama-soils/10p/barcodes.fastq.gz :saveas: emp-paired-end-sequences/barcodes.fastq.gz .. _`atacama demux`: @@ -253,4 +253,4 @@ Califf, Cesar Cardona, Audrey Copeland, Will van Treuren, Karen L. Josephson, Rob Knight, Jack A. Gilbert, Jay Quade, J. Gregory Caporaso, and Raina M. Maier. mSystems May 2017, 2 (3) e00195-16; DOI: 10.1128/mSystems.00195-16. -.. _sample metadata: https://data.qiime2.org/2024.10/tutorials/atacama-soils/sample_metadata +.. _sample metadata: https://data.qiime2.org/2024.5/tutorials/atacama-soils/sample_metadata diff --git a/source/tutorials/chimera.rst b/source/tutorials/chimera.rst index 8563267c..89c97a90 100644 --- a/source/tutorials/chimera.rst +++ b/source/tutorials/chimera.rst @@ -19,11 +19,11 @@ Start by creating a directory to work in. Next, download the necessary files: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/chimera/atacama-table.qza + :url: https://data.qiime2.org/2024.5/tutorials/chimera/atacama-table.qza :saveas: atacama-table.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/chimera/atacama-rep-seqs.qza + :url: https://data.qiime2.org/2024.5/tutorials/chimera/atacama-rep-seqs.qza :saveas: atacama-rep-seqs.qza Run *de novo* chimera checking diff --git a/source/tutorials/exporting.rst b/source/tutorials/exporting.rst index adebf9db..99371f75 100644 --- a/source/tutorials/exporting.rst +++ b/source/tutorials/exporting.rst @@ -17,7 +17,7 @@ Exporting a feature table A ``FeatureTable[Frequency]`` artifact will be exported as a `BIOM v2.1.0 formatted file`_. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/exporting/feature-table.qza + :url: https://data.qiime2.org/2024.5/tutorials/exporting/feature-table.qza :saveas: feature-table.qza .. command-block:: @@ -32,7 +32,7 @@ Exporting a phylogenetic tree A ``Phylogeny[Unrooted]`` artifact will be exported as a `newick formatted file`_. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/exporting/unrooted-tree.qza + :url: https://data.qiime2.org/2024.5/tutorials/exporting/unrooted-tree.qza :saveas: unrooted-tree.qza .. command-block:: diff --git a/source/tutorials/feature-classifier.rst b/source/tutorials/feature-classifier.rst index c6ea58ed..070bb189 100644 --- a/source/tutorials/feature-classifier.rst +++ b/source/tutorials/feature-classifier.rst @@ -25,11 +25,11 @@ Two elements are required for training the classifier: the reference sequences a We will also download the representative sequences from the `Moving Pictures`_ tutorial to test our classifier. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/training-feature-classifiers/85_otus.fasta + :url: https://data.qiime2.org/2024.5/tutorials/training-feature-classifiers/85_otus.fasta :saveas: 85_otus.fasta .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/training-feature-classifiers/85_otu_taxonomy.txt + :url: https://data.qiime2.org/2024.5/tutorials/training-feature-classifiers/85_otu_taxonomy.txt :saveas: 85_otu_taxonomy.txt Next we import these data into QIIME 2 Artifacts. Since the Greengenes reference taxonomy file (:file:`85_otu_taxonomy.txt`) is a tab-separated (TSV) file without a header, we must specify ``HeaderlessTSVTaxonomyFormat`` as the *source format* since the default *source format* requires a header. @@ -89,7 +89,7 @@ Test the classifier Finally, we verify that the classifier works by classifying the representative sequences from the `Moving Pictures`_ tutorial and visualizing the resulting taxonomic assignments. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/training-feature-classifiers/rep-seqs.qza + :url: https://data.qiime2.org/2024.5/tutorials/training-feature-classifiers/rep-seqs.qza :saveas: rep-seqs.qza .. command-block:: diff --git a/source/tutorials/filtering.rst b/source/tutorials/filtering.rst index 508f794b..c983a50e 100644 --- a/source/tutorials/filtering.rst +++ b/source/tutorials/filtering.rst @@ -19,23 +19,23 @@ First, create a directory to work in and change to that directory. Download the data we'll use in the tutorial. This includes sample metadata, a feature table, and a distance matrix: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/moving-pictures/sample_metadata.tsv + :url: https://data.qiime2.org/2024.5/tutorials/moving-pictures/sample_metadata.tsv :saveas: sample-metadata.tsv .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/filtering/table.qza + :url: https://data.qiime2.org/2024.5/tutorials/filtering/table.qza :saveas: table.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/filtering/distance-matrix.qza + :url: https://data.qiime2.org/2024.5/tutorials/filtering/distance-matrix.qza :saveas: distance-matrix.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/filtering/taxonomy.qza + :url: https://data.qiime2.org/2024.5/tutorials/filtering/taxonomy.qza :saveas: taxonomy.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/filtering/sequences.qza + :url: https://data.qiime2.org/2024.5/tutorials/filtering/sequences.qza :saveas: sequences.qza Filtering feature tables diff --git a/source/tutorials/fmt.rst b/source/tutorials/fmt.rst index 345a6552..92076003 100644 --- a/source/tutorials/fmt.rst +++ b/source/tutorials/fmt.rst @@ -25,7 +25,7 @@ Create a directory to work in called ``qiime2-fmt-tutorial`` and change to that As in the Moving Pictures study, you should begin your analysis by familiarizing yourself with the sample metadata. You can again access the `sample metadata`_ as a Google Spreadsheet. Notice that there are three tabs in this spreadsheet. This first tab (called sample-metadata) contains all of the clinical metadata. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/fmt/sample_metadata.tsv + :url: https://data.qiime2.org/2024.5/tutorials/fmt/sample_metadata.tsv :saveas: sample-metadata.tsv Next, download the *demultiplexed sequences* that we'll use in this analysis. To learn how to start a QIIME 2 analysis from fastq-formatted sequence data, see the :doc:`importing data tutorial `. We'll need to download two sets of demultiplexed sequences, each corresponding to one of the sequencing runs. @@ -38,23 +38,23 @@ In this tutorial we'll work with a small subsample of the complete sequence data .. download:: :no-exec: - :url: https://data.qiime2.org/2024.10/tutorials/fmt/fmt-tutorial-demux-1-10p.qza + :url: https://data.qiime2.org/2024.5/tutorials/fmt/fmt-tutorial-demux-1-10p.qza :saveas: fmt-tutorial-demux-1.qza .. download:: :no-exec: - :url: https://data.qiime2.org/2024.10/tutorials/fmt/fmt-tutorial-demux-2-10p.qza + :url: https://data.qiime2.org/2024.5/tutorials/fmt/fmt-tutorial-demux-2-10p.qza :saveas: fmt-tutorial-demux-2.qza 1% subsample data ~~~~~~~~~~~~~~~~~ .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/fmt/fmt-tutorial-demux-1-1p.qza + :url: https://data.qiime2.org/2024.5/tutorials/fmt/fmt-tutorial-demux-1-1p.qza :saveas: fmt-tutorial-demux-1.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/fmt/fmt-tutorial-demux-2-1p.qza + :url: https://data.qiime2.org/2024.5/tutorials/fmt/fmt-tutorial-demux-2-1p.qza :saveas: fmt-tutorial-demux-2.qza Sequence quality control @@ -185,5 +185,5 @@ Acknowledgements The data in this tutorial was initially presented in: Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Dae-Wook Kang, James B. Adams, Ann C. Gregory, Thomas Borody, Lauren Chittick, Alessio Fasano, Alexander Khoruts, Elizabeth Geis, Juan Maldonado, Sharon McDonough-Means, Elena L. Pollard, Simon Roux, Michael J. Sadowsky, Karen Schwarzberg Lipson, Matthew B. Sullivan, J. Gregory Caporaso and Rosa Krajmalnik-Brown. Microbiome (2017) 5:10. DOI: 10.1186/s40168-016-0225-7. .. _DADA2: https://www.ncbi.nlm.nih.gov/pubmed/27214047 -.. _sample metadata: https://data.qiime2.org/2024.10/tutorials/fmt/sample_metadata +.. _sample metadata: https://data.qiime2.org/2024.5/tutorials/fmt/sample_metadata .. _Fecal Microbiome Transplant study: http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0225-7 diff --git a/source/tutorials/importing.rst b/source/tutorials/importing.rst index be7f3d87..1d301428 100644 --- a/source/tutorials/importing.rst +++ b/source/tutorials/importing.rst @@ -62,11 +62,11 @@ Obtaining example data mkdir emp-single-end-sequences .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/moving-pictures/emp-single-end-sequences/barcodes.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/moving-pictures/emp-single-end-sequences/barcodes.fastq.gz :saveas: emp-single-end-sequences/barcodes.fastq.gz .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/moving-pictures/emp-single-end-sequences/sequences.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/moving-pictures/emp-single-end-sequences/sequences.fastq.gz :saveas: emp-single-end-sequences/sequences.fastq.gz Importing data @@ -105,15 +105,15 @@ Obtaining example data mkdir emp-paired-end-sequences .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/1p/forward.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/atacama-soils/1p/forward.fastq.gz :saveas: emp-paired-end-sequences/forward.fastq.gz .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/1p/reverse.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/atacama-soils/1p/reverse.fastq.gz :saveas: emp-paired-end-sequences/reverse.fastq.gz .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/1p/barcodes.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/atacama-soils/1p/barcodes.fastq.gz :saveas: emp-paired-end-sequences/barcodes.fastq.gz Importing data @@ -147,7 +147,7 @@ Obtaining example data mkdir muxed-se-barcode-in-seq .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/muxed-se-barcode-in-seq.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/importing/muxed-se-barcode-in-seq.fastq.gz :saveas: muxed-se-barcode-in-seq/sequences.fastq.gz Importing data @@ -192,11 +192,11 @@ Obtaining example data mkdir muxed-pe-barcode-in-seq .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/muxed-pe-barcode-in-seq/forward.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/importing/muxed-pe-barcode-in-seq/forward.fastq.gz :saveas: muxed-pe-barcode-in-seq/forward.fastq.gz .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/muxed-pe-barcode-in-seq/reverse.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/importing/muxed-pe-barcode-in-seq/reverse.fastq.gz :saveas: muxed-pe-barcode-in-seq/reverse.fastq.gz Importing data @@ -229,7 +229,7 @@ Obtaining example data `````````````````````` .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/casava-18-single-end-demultiplexed.zip + :url: https://data.qiime2.org/2024.5/tutorials/importing/casava-18-single-end-demultiplexed.zip :saveas: casava-18-single-end-demultiplexed.zip .. command-block:: @@ -266,7 +266,7 @@ Obtaining example data `````````````````````` .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/casava-18-paired-end-demultiplexed.zip + :url: https://data.qiime2.org/2024.5/tutorials/importing/casava-18-paired-end-demultiplexed.zip :saveas: casava-18-paired-end-demultiplexed.zip .. command-block:: @@ -324,11 +324,11 @@ SingleEndFastqManifestPhred33V2 In this variant of the fastq manifest format, the read directions must all either be forward or reverse. This format assumes that the `PHRED offset`_ used for the positional quality scores in all of the ``fastq.gz`` / ``fastq`` files is 33. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/se-33.zip + :url: https://data.qiime2.org/2024.5/tutorials/importing/se-33.zip :saveas: se-33.zip .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/se-33-manifest + :url: https://data.qiime2.org/2024.5/tutorials/importing/se-33-manifest :saveas: se-33-manifest .. command-block:: @@ -358,11 +358,11 @@ PairedEndFastqManifestPhred64V2 In this variant of the fastq manifest format, there must be forward and reverse read ``fastq.gz`` / ``fastq`` files for each sample ID. This format assumes that the `PHRED offset`_ used for the positional quality scores in all of the ``fastq.gz`` / ``fastq`` files is 64. During import, QIIME 2 will convert the PHRED 64 encoded quality scores to PHRED 33 encoded quality scores. This conversion will be slow, but will only happen one time. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/pe-64.zip + :url: https://data.qiime2.org/2024.5/tutorials/importing/pe-64.zip :saveas: pe-64.zip .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/pe-64-manifest + :url: https://data.qiime2.org/2024.5/tutorials/importing/pe-64-manifest :saveas: pe-64-manifest .. command-block:: @@ -396,7 +396,7 @@ Obtaining example data ********************** .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/sequences.fna + :url: https://data.qiime2.org/2024.5/tutorials/importing/sequences.fna :saveas: sequences.fna Importing data @@ -421,7 +421,7 @@ Obtaining example data ********************** .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/aligned-sequences.fna + :url: https://data.qiime2.org/2024.5/tutorials/importing/aligned-sequences.fna :saveas: aligned-sequences.fna Importing data @@ -453,7 +453,7 @@ Obtaining example data `````````````````````` .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/feature-table-v100.biom + :url: https://data.qiime2.org/2024.5/tutorials/importing/feature-table-v100.biom :saveas: feature-table-v100.biom Importing data @@ -479,7 +479,7 @@ Obtaining example data `````````````````````` .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/feature-table-v210.biom + :url: https://data.qiime2.org/2024.5/tutorials/importing/feature-table-v210.biom :saveas: feature-table-v210.biom Importing data @@ -505,7 +505,7 @@ Obtaining example data ********************** .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/importing/unrooted-tree.tre + :url: https://data.qiime2.org/2024.5/tutorials/importing/unrooted-tree.tre :saveas: unrooted-tree.tre Importing data diff --git a/source/tutorials/longitudinal.rst b/source/tutorials/longitudinal.rst index 2cbcfffc..1f89dc97 100644 --- a/source/tutorials/longitudinal.rst +++ b/source/tutorials/longitudinal.rst @@ -22,15 +22,15 @@ In the examples below, we use data from the `ECAM study`_, a longitudinal study cd longitudinal-tutorial .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/longitudinal/sample_metadata.tsv + :url: https://data.qiime2.org/2024.5/tutorials/longitudinal/sample_metadata.tsv :saveas: ecam-sample-metadata.tsv .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/longitudinal/ecam_shannon.qza + :url: https://data.qiime2.org/2024.5/tutorials/longitudinal/ecam_shannon.qza :saveas: shannon.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/longitudinal/unweighted_unifrac_distance_matrix.qza + :url: https://data.qiime2.org/2024.5/tutorials/longitudinal/unweighted_unifrac_distance_matrix.qza :saveas: unweighted_unifrac_distance_matrix.qza @@ -209,7 +209,7 @@ Within microbial communities, microbial populations do not exist in isolation bu First let's download a feature table to test. Here we will test genus-level taxa that exhibit a relative abundance > 0.1% in more than 15% of the total samples. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/longitudinal/ecam_table_taxa.qza + :url: https://data.qiime2.org/2024.5/tutorials/longitudinal/ecam_table_taxa.qza :saveas: ecam-table-taxa.qza Now we are ready run NMIT. The output of this command is a distance matrix that we can pass to other QIIME2 commands for significance testing and visualization. @@ -264,7 +264,7 @@ This pipeline identifies features that are predictive of a numeric metadata colu Let's test this out on the ECAM dataset. First download a table to work with: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/longitudinal/ecam_table_maturity.qza + :url: https://data.qiime2.org/2024.5/tutorials/longitudinal/ecam_table_maturity.qza :saveas: ecam-table.qza .. command-block:: diff --git a/source/tutorials/metadata.rst b/source/tutorials/metadata.rst index 14adf560..0a620ec5 100644 --- a/source/tutorials/metadata.rst +++ b/source/tutorials/metadata.rst @@ -191,7 +191,7 @@ To get started with understanding sample metadata files, download an example TSV cd qiime2-metadata-tutorial .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/moving-pictures/sample_metadata.tsv + :url: https://data.qiime2.org/2024.5/tutorials/moving-pictures/sample_metadata.tsv :saveas: sample-metadata.tsv Since this is a TSV file, it can be opened and edited in a variety of applications, including text editors, Microsoft Excel, and Google Sheets (e.g. if you plan to validate your metadata with Keemei_). @@ -216,7 +216,7 @@ In addition to TSV metadata files, QIIME 2 also supports viewing some kinds of a To get started with understanding artifacts as metadata, first download an example artifact: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/metadata/faith_pd_vector.qza + :url: https://data.qiime2.org/2024.5/tutorials/metadata/faith_pd_vector.qza :saveas: faith_pd_vector.qza To view this artifact as metadata, simply pass it in to any method or visualizer that expects to see metadata (e.g. ``metadata tabulate`` or ``emperor plot``): @@ -253,7 +253,7 @@ The resulting metadata after the merge will contain the intersection of the iden Metadata merging is supported anywhere that metadata is accepted in QIIME 2. For example, it might be interesting to color an Emperor plot based on the study metadata, or sample alpha diversity. This can be accomplished by providing both the sample metadata file *and* the ``SampleData[AlphaDiversity]`` artifact: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/metadata/unweighted_unifrac_pcoa_results.qza + :url: https://data.qiime2.org/2024.5/tutorials/metadata/unweighted_unifrac_pcoa_results.qza :saveas: unweighted_unifrac_pcoa_results.qza .. command-block:: @@ -277,11 +277,11 @@ Metadata in QIIME 2 can be applied to sample or features --- so far we have only To get started with feature metadata, first download the example files: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/metadata/rep-seqs.qza + :url: https://data.qiime2.org/2024.5/tutorials/metadata/rep-seqs.qza :saveas: rep-seqs.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/metadata/taxonomy.qza + :url: https://data.qiime2.org/2024.5/tutorials/metadata/taxonomy.qza :saveas: taxonomy.qza We have downloaded a ``FeatureData[Sequence]`` file (``rep-seqs.qza``) and a ``FeatureData[Taxonomy]`` file (``taxonomy.qza``). We can merge (and ``tabulate``) these files to associate the representative sequences with their taxonomic annotations: @@ -312,6 +312,6 @@ Finally, there are export options available in the visualizations produced from .. _`cual-id`: http://msystems.asm.org/content/1/1/e00010-15 .. _`Phylip`: http://evolution.genetics.washington.edu/phylip.html .. _`Python csv module`: https://docs.python.org/3/library/csv.html -.. _`evenness vector`: https://docs.qiime2.org/2024.10/data/tutorials/moving-pictures/core-metrics-results/evenness_vector.qza -.. _`feature table artifact`: https://docs.qiime2.org/2024.10/data/tutorials/moving-pictures/table.qza -.. _`QIIME 2 Utilities`: https://docs.qiime2.org/2024.10/tutorials/utilities +.. _`evenness vector`: https://docs.qiime2.org/2024.5/data/tutorials/moving-pictures/core-metrics-results/evenness_vector.qza +.. _`feature table artifact`: https://docs.qiime2.org/2024.5/data/tutorials/moving-pictures/table.qza +.. _`QIIME 2 Utilities`: https://docs.qiime2.org/2024.5/tutorials/utilities diff --git a/source/tutorials/moving-pictures-usage.rst b/source/tutorials/moving-pictures-usage.rst index aba41a0a..7202ca45 100644 --- a/source/tutorials/moving-pictures-usage.rst +++ b/source/tutorials/moving-pictures-usage.rst @@ -48,7 +48,7 @@ tab-separated text and save it in the file ``sample-metadata.tsv``. This from urllib import request from qiime2 import Metadata fp, _ = request.urlretrieve( - 'https://data.qiime2.org/2024.10/tutorials/moving-pictures/sample_metadata.tsv', + 'https://data.qiime2.org/2024.5/tutorials/moving-pictures/sample_metadata.tsv', ) return Metadata.load(fp) @@ -84,7 +84,7 @@ commands will run quickly. from q2_types.multiplexed_sequences._format import EMPSingleEndDirFmt from q2_types.per_sample_sequences import FastqGzFormat - base_url = 'https://data.qiime2.org/2024.10/tutorials/moving-pictures/' + base_url = 'https://data.qiime2.org/2024.5/tutorials/moving-pictures/' bc_url = base_url + 'emp-single-end-sequences/barcodes.fastq.gz' seqs_url = base_url + 'emp-single-end-sequences/sequences.fastq.gz' @@ -798,7 +798,7 @@ from sequence to taxonomy. from urllib import request from qiime2 import Artifact fp, _ = request.urlretrieve( - 'https://data.qiime2.org/2024.10/common/gg-13-8-99-515-806-nb-classifier.qza', + 'https://data.qiime2.org/2024.5/common/gg-13-8-99-515-806-nb-classifier.qza', ) return Artifact.load(fp) @@ -938,7 +938,7 @@ level (i.e. level 6 of the Greengenes taxonomy). .. g__Parabacteroides (enriched), g__Paraprevotella (depleted) .. We see more differentially abundant features in the original compared to the collapsed table, which is reasonable since we are collapsing at the genus level and thus losing some resolution. However, collapsing at level 6 may allow us to investigate patterns that aren't present when looking at ASVs. -.. _sample metadata: https://data.qiime2.org/2024.10/tutorials/moving-pictures/sample_metadata +.. _sample metadata: https://data.qiime2.org/2024.5/tutorials/moving-pictures/sample_metadata .. _Keemei: https://keemei.qiime2.org .. _DADA2: https://www.ncbi.nlm.nih.gov/pubmed/27214047 .. _Illumina Overview Tutorial: http://nbviewer.jupyter.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb diff --git a/source/tutorials/moving-pictures.rst b/source/tutorials/moving-pictures.rst index 009c0566..f3c5db25 100644 --- a/source/tutorials/moving-pictures.rst +++ b/source/tutorials/moving-pictures.rst @@ -24,7 +24,7 @@ Sample metadata Before starting the analysis, explore the sample metadata to familiarize yourself with the samples used in this study. The `sample metadata`_ is available as a Google Sheet. You can download this file as tab-separated text by selecting ``File`` > ``Download as`` > ``Tab-separated values``. Alternatively, the following command will download the sample metadata as tab-separated text and save it in the file ``sample-metadata.tsv``. This ``sample-metadata.tsv`` file is used throughout the rest of the tutorial. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/moving-pictures/sample_metadata.tsv + :url: https://data.qiime2.org/2024.5/tutorials/moving-pictures/sample_metadata.tsv :saveas: sample-metadata.tsv .. tip:: `Keemei`_ is a Google Sheets add-on for validating sample metadata. Validation of sample metadata is important before beginning any analysis. Try installing Keemei following the instructions on its website, and then validate the sample metadata spreadsheet linked above. The spreadsheet also includes a sheet with some invalid data to try out with Keemei. @@ -41,11 +41,11 @@ Download the sequence reads that we'll use in this analysis. In this tutorial we mkdir emp-single-end-sequences .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/moving-pictures/emp-single-end-sequences/barcodes.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/moving-pictures/emp-single-end-sequences/barcodes.fastq.gz :saveas: emp-single-end-sequences/barcodes.fastq.gz .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/moving-pictures/emp-single-end-sequences/sequences.fastq.gz + :url: https://data.qiime2.org/2024.5/tutorials/moving-pictures/emp-single-end-sequences/sequences.fastq.gz :saveas: emp-single-end-sequences/sequences.fastq.gz All data that is used as input to QIIME 2 is in form of QIIME 2 artifacts, which contain information about the type of data and the source of the data. So, the first thing we need to do is import these sequence data files into a QIIME 2 artifact. @@ -383,7 +383,7 @@ In the next sections we'll begin to explore the taxonomic composition of the sam .. download:: - :url: https://data.qiime2.org/2024.10/common/gg-13-8-99-515-806-nb-classifier.qza + :url: https://data.qiime2.org/2024.5/common/gg-13-8-99-515-806-nb-classifier.qza :saveas: gg-13-8-99-515-806-nb-classifier.qza .. command-block:: @@ -488,7 +488,7 @@ We're also often interested in performing a differential abundance test at a spe .. g__Parabacteroides (enriched), g__Paraprevotella (depleted) .. We see more differentially abundant features in the original compared to the collapsed table, which is reasonable since we are collapsing at the genus level and thus losing some resolution. However, collapsing at level 6 may allow us to investigate patterns that aren't present when looking at ASVs. -.. _sample metadata: https://data.qiime2.org/2024.10/tutorials/moving-pictures/sample_metadata +.. _sample metadata: https://data.qiime2.org/2024.5/tutorials/moving-pictures/sample_metadata .. _Keemei: https://keemei.qiime2.org .. _DADA2: https://www.ncbi.nlm.nih.gov/pubmed/27214047 .. _Illumina Overview Tutorial: http://nbviewer.jupyter.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb diff --git a/source/tutorials/otu-clustering.rst b/source/tutorials/otu-clustering.rst index 1d728355..836f7d88 100644 --- a/source/tutorials/otu-clustering.rst +++ b/source/tutorials/otu-clustering.rst @@ -41,11 +41,11 @@ Start by creating a directory to work in. Next, download the necessary files: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/otu-clustering/seqs.fna + :url: https://data.qiime2.org/2024.5/tutorials/otu-clustering/seqs.fna :saveas: seqs.fna .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/otu-clustering/85_otus.qza + :url: https://data.qiime2.org/2024.5/tutorials/otu-clustering/85_otus.qza :saveas: 85_otus.qza Dereplicating a ``SampleData[Sequences]`` artifact diff --git a/source/tutorials/overview.rst b/source/tutorials/overview.rst index b3a8b45f..982542f3 100644 --- a/source/tutorials/overview.rst +++ b/source/tutorials/overview.rst @@ -278,8 +278,8 @@ Now go forth an have fun! 💃 .. _q2-phylogeny tutorial: https://forum.qiime2.org/t/q2-phylogeny-community-tutorial/4455 .. _q2-fragment-insertion tutorial: https://library.qiime2.org/plugins/q2-fragment-insertion/16/ .. _diversity metrics: https://forum.qiime2.org/t/alpha-and-beta-diversity-explanations-and-commands/2282 -.. _q2-feature-table: https://docs.qiime2.org/2024.10/plugins/available/feature-table/ -.. _many different useful actions: https://docs.qiime2.org/2024.10/plugins/available/diversity/ +.. _q2-feature-table: https://docs.qiime2.org/2024.5/plugins/available/feature-table/ +.. _many different useful actions: https://docs.qiime2.org/2024.5/plugins/available/diversity/ .. _Principal coordinates analysis: https://mb3is.megx.net/gustame/dissimilarity-based-methods/principal-coordinates-analysis .. _longitudinal experiments: https://en.wikipedia.org/wiki/Longitudinal_study .. _predict cancer susceptibility: https://dx.doi.org/10.1128%2FmSphere.00001-15 diff --git a/source/tutorials/pd-mice.rst b/source/tutorials/pd-mice.rst index 6d7847ce..da667531 100644 --- a/source/tutorials/pd-mice.rst +++ b/source/tutorials/pd-mice.rst @@ -105,7 +105,7 @@ Even though the mouse ID looks like a number, we will specify that it is categor The metadata is available as a `Google Sheet`_, or you can download it directly and save it as a TSV (tab-separated values) file. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/pd-mice/sample_metadata.tsv + :url: https://data.qiime2.org/2024.5/tutorials/pd-mice/sample_metadata.tsv :saveas: metadata.tsv The sample metadata will be used throughout the tutorial. Let's run our first QIIME 2 command, to summarize and explore the metadata. @@ -130,11 +130,11 @@ We will import the sequences as ``SampleData[SequencesWithQuality]``, which is t Let's start by downloading the manifest and corresponding sequences. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/pd-mice/manifest + :url: https://data.qiime2.org/2024.5/tutorials/pd-mice/manifest :saveas: manifest.tsv .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/pd-mice/demultiplexed_seqs.zip + :url: https://data.qiime2.org/2024.5/tutorials/pd-mice/demultiplexed_seqs.zip :saveas: demultiplexed_seqs.zip You'll need to unzip sequence archive you just downloaded: @@ -269,7 +269,7 @@ QIIME 2 offers several ways to construct a phylogenetic tree. For this tutorial, First, we will download the reference database: .. download:: - :url: https://data.qiime2.org/2024.10/common/sepp-refs-gg-13-8.qza + :url: https://data.qiime2.org/2024.5/common/sepp-refs-gg-13-8.qza :saveas: sepp-refs-gg-13-8.qza .. note:: @@ -528,7 +528,7 @@ Up until now we have been performing diversity analyses directly on ASVs; in oth For this analysis, we'll use a pre-trained naive Bayes machine-learning classifier that was trained to differentiate taxa present in the 99% Greengenes 13_8 reference set trimmed to 250 bp of the V4 hypervariable region (corresponding to the 515F-806R primers). `This classifier works`_ by identifying k-mers that are diagnostic for particular taxonomic groups, and using that information to predict the taxonomic affiliation of each ASV. We can download the pre-trained classifier here: .. download:: - :url: https://data.qiime2.org/2024.10/common/gg-13-8-99-515-806-nb-classifier.qza + :url: https://data.qiime2.org/2024.5/common/gg-13-8-99-515-806-nb-classifier.qza :saveas: gg-13-8-99-515-806-nb-classifier.qza It's worth noting that Naive Bayes classifiers perform best when they're trained for the specific hypervariable region amplified. You can train a classifier specific for your dataset based on the :doc:`training classifiers tutorial ` or download classifiers for other datasets from the :doc:`QIIME 2 resource page <../data-resources>`. Classifiers can be re-used for consistent versions of the underlying packages, database, and region of interest. @@ -693,15 +693,15 @@ If you feel that these samples are not typical stool samples, it is possible to, Start by downloading the stool data, along with the 99% Greengene 13_8 reference data. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/pd-mice/ref_seqs_v4.qza + :url: https://data.qiime2.org/2024.5/tutorials/pd-mice/ref_seqs_v4.qza :saveas: ref_seqs_v4.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/pd-mice/ref_tax.qza + :url: https://data.qiime2.org/2024.5/tutorials/pd-mice/ref_tax.qza :saveas: ref_tax.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/pd-mice/animal_distal_gut.qza + :url: https://data.qiime2.org/2024.5/tutorials/pd-mice/animal_distal_gut.qza :saveas: animal_distal_gut.qza Next retrain the classifier. @@ -943,7 +943,7 @@ This suggests that there is a genotype-specific effect on the microbiome of mice .. _PERMANOVA: https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1442-9993.2001.01070.pp.x .. _This classifier works: https://doi.org/10.1186/s40168-018-0470-z .. _ANCOM-BC paper: https://pubmed.ncbi.nlm.nih.gov/32665548/ -.. _Google Sheet: https://data.qiime2.org/2024.10/tutorials/pd-mice/sample_metadata +.. _Google Sheet: https://data.qiime2.org/2024.5/tutorials/pd-mice/sample_metadata .. _permdisp: https://www.ncbi.nlm.nih.gov/pubmed/16706913 .. _volcano plot: https://en.wikipedia.org/wiki/Volcano_plot_(statistics) .. _confusion matrix: https://en.wikipedia.org/wiki/Confusion_matrix diff --git a/source/tutorials/phylogeny.rst b/source/tutorials/phylogeny.rst index fefe5171..2bb438a7 100644 --- a/source/tutorials/phylogeny.rst +++ b/source/tutorials/phylogeny.rst @@ -71,7 +71,7 @@ Let's start by creating a directory to work in: Next, download the data: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/phylogeny/rep-seqs.qza + :url: https://data.qiime2.org/2024.5/tutorials/phylogeny/rep-seqs.qza :saveas: rep-seqs.qza **Run MAFFT** diff --git a/source/tutorials/qiime2-for-experienced-microbiome-researchers.rst b/source/tutorials/qiime2-for-experienced-microbiome-researchers.rst index 418ef551..19138425 100644 --- a/source/tutorials/qiime2-for-experienced-microbiome-researchers.rst +++ b/source/tutorials/qiime2-for-experienced-microbiome-researchers.rst @@ -44,7 +44,7 @@ Alternatively, you can also unzip your artifact directly (``unzip -k file.qza``) **Pro-tip #2: the QIIME 2 command line interface tools are slow because they have to unzip and re-zip the data contained in the artifacts each time you call them.** If you need to process your data more interactively, you might want to use the Python API - it is much faster since objects can be simply stored in memory. -You can learn more about the different `QIIME 2 interfaces `__. +You can learn more about the different `QIIME 2 interfaces `__. Data processing steps --------------------- diff --git a/source/tutorials/quality-control.rst b/source/tutorials/quality-control.rst index 2da5633f..44f8e8cd 100644 --- a/source/tutorials/quality-control.rst +++ b/source/tutorials/quality-control.rst @@ -16,23 +16,23 @@ We will download and create several files, so first create a working directory. Let's download some example data and get started. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/quality-control/query-seqs.qza + :url: https://data.qiime2.org/2024.5/tutorials/quality-control/query-seqs.qza :saveas: query-seqs.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/quality-control/reference-seqs.qza + :url: https://data.qiime2.org/2024.5/tutorials/quality-control/reference-seqs.qza :saveas: reference-seqs.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/quality-control/query-table.qza + :url: https://data.qiime2.org/2024.5/tutorials/quality-control/query-table.qza :saveas: query-table.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/quality-control/qc-mock-3-expected.qza + :url: https://data.qiime2.org/2024.5/tutorials/quality-control/qc-mock-3-expected.qza :saveas: qc-mock-3-expected.qza .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/quality-control/qc-mock-3-observed.qza + :url: https://data.qiime2.org/2024.5/tutorials/quality-control/qc-mock-3-observed.qza :saveas: qc-mock-3-observed.qza diff --git a/source/tutorials/read-joining.rst b/source/tutorials/read-joining.rst index b8cb4782..263a9a7f 100644 --- a/source/tutorials/read-joining.rst +++ b/source/tutorials/read-joining.rst @@ -40,7 +40,7 @@ artifact, which contains the demultiplexed reads from the :doc:`Atacama soil microbiome tutorial `. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/read-joining/atacama-seqs.qza + :url: https://data.qiime2.org/2024.5/tutorials/read-joining/atacama-seqs.qza :saveas: demux.qza Joining reads @@ -166,7 +166,7 @@ First, download the following demultiplexed and joined read data, which has been joined on a per-sample basis with ``fastq-join``. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/read-joining/fj-joined.zip + :url: https://data.qiime2.org/2024.5/tutorials/read-joining/fj-joined.zip :saveas: fj-joined.zip Unzip this file as follows: diff --git a/source/tutorials/sample-classifier.rst b/source/tutorials/sample-classifier.rst index 62624c85..caad0b35 100644 --- a/source/tutorials/sample-classifier.rst +++ b/source/tutorials/sample-classifier.rst @@ -23,11 +23,11 @@ Predicting categorical sample data Supervised learning classifiers predict the categorical metadata classes of unlabeled samples by learning the composition of labeled training samples. For example, we may use a classifier to diagnose or predict disease susceptibility based on stool microbiome composition, or predict sample type as a function of the sequence variants, microbial taxa, or metabolites detected in a sample. In this tutorial, we will use the :doc:`moving pictures tutorial data ` to train a classifier that predicts the body site from which a sample was collected. Download the feature table and sample metadata with the following links: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/moving-pictures/sample_metadata.tsv + :url: https://data.qiime2.org/2024.5/tutorials/moving-pictures/sample_metadata.tsv :saveas: moving-pictures-sample-metadata.tsv .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/sample-classifier/moving-pictures-table.qza + :url: https://data.qiime2.org/2024.5/tutorials/sample-classifier/moving-pictures-table.qza :saveas: moving-pictures-table.qza Next, we will train and test a classifier that predicts which body site a sample originated from based on its microbial composition. We will do so using the ``classify-samples`` pipeline, which performs a series of steps under the hood: @@ -181,11 +181,11 @@ Predicting continuous (i.e., numerical) sample data Supervised learning regressors predict continuous metadata values of unlabeled samples by learning the composition of labeled training samples. For example, we may use a regressor to predict the abundance of a metabolite that will be produced by a microbial community, or a sample's pH, temperature, or altitude as a function of the sequence variants, microbial taxa, or metabolites detected in a sample. In this tutorial, we will use the `ECAM study`_, a longitudinal cohort study of microbiome development in U.S. infants. Download the feature table and sample metadata with the following links: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/longitudinal/sample_metadata.tsv + :url: https://data.qiime2.org/2024.5/tutorials/longitudinal/sample_metadata.tsv :saveas: ecam-metadata.tsv .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/longitudinal/ecam_table_maturity.qza + :url: https://data.qiime2.org/2024.5/tutorials/longitudinal/ecam_table_maturity.qza :saveas: ecam-table.qza Next, we will train a regressor to predict an infant's age based on its microbiota composition, using the ``regress-samples`` pipeline. diff --git a/source/tutorials/utilities.rst b/source/tutorials/utilities.rst index e183e7c7..e2790586 100644 --- a/source/tutorials/utilities.rst +++ b/source/tutorials/utilities.rst @@ -25,7 +25,7 @@ functionality! First, we will take a look at the taxonomic bar charts from the :doc:`PD Mice Tutorial `: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/utilities/taxa-barplot.qzv + :url: https://data.qiime2.org/2024.5/tutorials/utilities/taxa-barplot.qzv :saveas: taxa-barplot.qzv Retrieving Citations @@ -100,7 +100,7 @@ Oftentimes we need to verify the ``type`` and ``uuid`` of an Artifact. We can us let's get some data to look at: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/utilities/faith-pd-vector.qza + :url: https://data.qiime2.org/2024.5/tutorials/utilities/faith-pd-vector.qza :saveas: faith-pd-vector.qza Now that we have data, we can learn more about the file: @@ -140,7 +140,7 @@ are in the file? We can demonstrate this by first downloading some sample metadata: .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/pd-mice/sample_metadata.tsv + :url: https://data.qiime2.org/2024.5/tutorials/pd-mice/sample_metadata.tsv :saveas: sample-metadata.tsv Then, we can run the ``qiime tools inspect-metadata`` command: @@ -160,7 +160,7 @@ This tool can be very helpful for learning about Metadata column names for files that are *viewable* as Metadata. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/utilities/jaccard-pcoa.qza + :url: https://data.qiime2.org/2024.5/tutorials/utilities/jaccard-pcoa.qza :saveas: jaccard-pcoa.qza The file we just downloaded is a Jaccard PCoA (from the @@ -190,7 +190,7 @@ metadata used in the **Inspect Metadata** section, so you can skip this step if already downloaded the ``sample_metadata.tsv`` file from above. .. download:: - :url: https://data.qiime2.org/2024.10/tutorials/pd-mice/sample_metadata.tsv + :url: https://data.qiime2.org/2024.5/tutorials/pd-mice/sample_metadata.tsv :saveas: sample_metadata.tsv In this example, we will cast the ``days_post_transplant`` column from ``numeric`` to From 5fbd5ccf75bc958b52e3a42435146b502f51509e Mon Sep 17 00:00:00 2001 From: Liz Gehret Date: Wed, 5 Jun 2024 10:48:21 -0700 Subject: [PATCH 4/4] IMP: adds info for multi-distro Docker images --- source/install/virtual/docker.rst | 16 ++++++++++++---- source/install/virtual/index.rst | 2 +- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/source/install/virtual/docker.rst b/source/install/virtual/docker.rst index 799bc5bf..3069c58e 100644 --- a/source/install/virtual/docker.rst +++ b/source/install/virtual/docker.rst @@ -1,20 +1,28 @@ Installing QIIME 2 using Docker =============================== +The following QIIME 2 distributions are available as Docker images: + +- ``amplicon`` +- ``metagenome`` +- ``tiny`` + +Please replace with your desired distribution in the installation instructions below. + 1. Set up Docker ---------------- See https://www.docker.com for details. -2. Download QIIME 2 Image -------------------------- +2. Download desired QIIME 2 Distribution Image +---------------------------------------------- In a terminal with Docker activated, run: .. command-block:: :no-exec: - docker pull quay.io/qiime2/amplicon:2024.5 + docker pull quay.io/qiime2/:2024.5 3. Confirm the installation --------------------------- @@ -24,4 +32,4 @@ Run the following to confirm that the image was successfully fetched. .. command-block:: :no-exec: - docker run -t -i -v $(pwd):/data quay.io/qiime2/amplicon:2024.5 qiime + docker run -t -i -v $(pwd):/data quay.io/qiime2/:2024.5 qiime diff --git a/source/install/virtual/index.rst b/source/install/virtual/index.rst index 27f2a9b0..010d09b8 100644 --- a/source/install/virtual/index.rst +++ b/source/install/virtual/index.rst @@ -1,7 +1,7 @@ Installing QIIME 2 using a Virtual Machine ========================================== -*QIIME 2 Amplicon Distribution* builds are available as Docker Images. See :ref:`distributions` for more details about the Amplicon Distribution. +*QIIME 2 Distribution* builds are available as Docker Images. See :ref:`distributions` for more details about the available distributions. .. toctree:: :maxdepth: 1