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INSTALL_DEVSERVER.md

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NeuroVault Dev Server with Puppet, Vagrant, and VirtualBox

This guide will create an automated build of a NeuroVault dev environment (the VM) using three very useful tools:

  • Puppet is a server configuration management system
  • Vagrant is a virtual machine provisioning abstraction layer
  • VirtualBox is a freely available virtualization engine

1. Install Virtualbox and Vagrant

Install VirtualBox and Vagrant for your OS:

Install plugin for managing NFS permissions (if you want to use default settings)

vagrant plugin install vagrant-bindfs

(Optional) After installing Vagrant install vagrant-cachier which will speed up rebuilding of the VM:

vagrant plugin install vagrant-cachier

2. Setup A Vagrant project directory

  • Create, then enter a new directory on your computer (the Host) that will contain your Vagrant project:

    mkdir -p ~/vms/neurovault
cd ~/vms/neurovault

    This directory will contain all project resources: Git-tracked project source code, project media, server configuration manifests, and VM configuration.

  • Clone the NeuroVault puppet repository (this repo) to your vagrant directory:

    git clone https://github.com/NeuroVault/neurovault_puppet.git

  • Copy the Vagrantfile for Virtualbox to the root of the project directory:

    cp neurovault_puppet/confs/Vagrantfile.virtualbox Vagrantfile

  • Optional: Edit the Vagrantfile and customize it to your needs. (There is usually no need to modify this.)

    • The default config will use the simplest networking and file sharing option available for VirtualBox (Port Forwarding, and NFS). The options should work on most systems that can use Vagrant and provide reasonable performance.
    • See the detailed comments in the Vagrantfile for possible customization options.

3. Edit Puppet configuration

Edit confs/nvault.pp to configure NeuroVault for installation. Only a few settings require changes:

  • gmail_login_str to enable outgoing mail on the VM via a Google account.

  • skip_freesurfer to choose if Freesurfer will be installed

  • freesurfer_lic_* Freesurfer license key (3 lines)

See the comments in the config file for details, or to customize other settings.

Note: If you don't need a functional outgoing mailer or Freesurfer, you can simply set skip_freesurfer => true, and proceed to step 4. (Note that Pycortex will not be functional without Freesurfer.)

    
    # Gmail SMTP setting:  Enter a Gmail username and password in this format
    #  to specify a Google account to use for the server's outgoing mail.  You
    #  can create an account specifically for this purpose, or use an existing
    #  personal gmail account.
    # Note:  When creating a new Google account to use for outgoing SMTP,
    #  you'll need to log in, send an email, and receive an email as a normal
    #  web user before the account can be used programatically.
    
    gmail_login_str => "[email protected]:thepassword",
    
    # Set this to 'True' to skip Freesurfer altogether:
    skip_freesurfer => false,
    
    # Freesurfer license settings.  Freesurfer requires seperate user
    #  registration as non-free software.  Go to
    #  https://surfer.nmr.mgh.harvard.edu/registration.html to register for a
    #  free Freesurfer license key.  The three lines of the license file you
    #  receive in the email are placed into the following variables.  Note
    #  that the actual license string of encrypted characters contains a
    #  leading space.
    
    freesurfer_lic_email => "[email protected]",
    freesurfer_lic_id => "00000",
    freesurfer_lic_key => " 000000000", # leading space then 13char key

4. Vagrant Up

Now, we're ready to launch the VM. Vagrant and Puppet will create a fully automated installation. From your Vagrant project directory, enter:

vagrant up

The installation will take anywhere from 30 minutes to 3 hours, depending on performance, network conditions, and whether Freesurfer will be installed (4GB).

5. Using the VM

Vagrant will inform you when the installation is complete.

Accessing the VM:

=> To SSH into your VM, type vagrant ssh. => To access the site, go to http://192.168.33.10 in your Host OS browser.

Note: Everything is done as the vagrant user account, which has has sudo privileges without password.

File locations:

  • Django App: Your python environment and NeuroVault git working repositories will be located at ~/vms/neurovault/nv_env on your host machine. You can develop from this location, and changes will be synced to the VM.

  • Image Data: The site's image data directory will be served from ~/vms/neurovault/image_data on the Host OS.

  • Pycortex Data: The site's pycortex datastore will be served from ~/vms/neurovault/pycortex_data on the Host OS.

Django Devserver:

The system is deployed in basic production configuration by default, with Nginx and uwsgi running. To run and debug Neurovault with the Django dev server, do the following:

  • Stop Nginx and uwsgi:

    sudo service nginx stop
sudo service uwsgi stop

  • Navigate to the NeuroVault virtual environment and activate it:

    cd /opt/nv_env/
source bin/activate

  • Enter the Django root dir:

    cd NeuroVault

  • Start the Dev server on port 8080:

    ./manage.py runserver 0.0.0.0:8080

  • To access the running Dev server, go to http://localhost:8001 in your Host OS Browser (Port 8001 is used for the devserver, and 8000 is used for Nginx.)

6. Complete!

You should now be able to create a login, create a collection, and start testing NeuroVault! :shipit:

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