wiki:GalaxyUsage
Last modified 9 years ago Last modified on 05/04/11 17:58:40

Installing galaxy tools

  1. Login to cheaha using blazerid and password.
  2. Run following command to load galaxy specific python and other necessary environment variables.
    module load galaxy/galaxy
    
  3. This should load python 2.6.6 in your shell environment and also set other variables such as: $GALAXY_BASEDIR $GALAXY_INSTALL $GALAXY_PYTHON $GALAXY_TOOLS. Note that environment variables are for our convenience and not necessary for actual galaxy usage.
  4. The GALAXY_BASEDIR is set to /share/apps/galaxy directory. Do ls command to see it's directory contents.

Recommended way for installing tools

  1. Downloaded/copy archive/zip files of various tools in $GALAXY_BASEDIR/archives directory.
  2. Extract archived files in $GALAXY_BASEDIR/src directory.
  3. Install these tools in $GALAXY_BASEDIR/galaxy-tools directory.
  4. Confirm with system-admin if you need to make any changes to universe_wsgi.ini file. I think typically you (galaxy tool installer/users) shouldn't require to make any changes to this file. We will change this policy if we discover any shortcomings.

Browser or Web interface

Once we have galaxy firewalls rules working then you should be able to access galaxy.uabgrid.uab.edu using your blazerid-password. As a temporary workaround we will use ssh port forwarding for this purpose. Following steps should allow you to access galaxy via web interface.

  1. From your Mac or Linux system ssh to cheaha using your blazerid-password as follows:
    ssh -L 10080:galaxy.vm.ip.addr:80 cheaha.uabgrid.uab.edu
    
  2. Above command connects/tunnels your local system's port 10080 to galaxy.vm.ip.address's port 80. Now in your web browser type in http://localhost:10080/ . You should get a password prompt at this point. Login with a temporary password mailed to you. We will replace this with blazerid based authentication once we make our system public.

FAQ

  1. Where is galaxy running?

Galaxy is running on a separate VM within our cluster environment, but not on cheaha.

  1. How will galaxy recognize any changes that I make in /share/apps/galaxy on cheaha?

The GALAXY_BASEDIR, i.e., /share/apps/galaxy is a shared filesystem (NFS). It is visible by both cheaha and galaxy VM as well. Any changes you make to underlying directories/files will be available to galaxy VM as well - it's the same filesystem. Although they share the same filesystem space, the actual galaxy process (run.sh script) is running on the galaxy VM and not cheaha.

  1. How do I access galaxy VM?

At this point you shouldn't need any system level access to the galaxy VM. You can access galaxy using web interface though. If you need to install any tools then you will be using cheaha as explained above.

  1. Are we using lustre for storing files?

Nope, but it's coming soon. It shouldn't affect any of the galaxy tools installation. It should be a simple filesystem redirect (symlink).

... more coming...