Galaxy on UPPMAX, simplified

Roman Valls Guimerà bio photo By Roman Valls Guimerà Comment

This post is intended to be shortened over time, eventually becoming an automated procedure… a wiki-post from dahlo’s magic until upstream patches settle down. All commands are issued on the cluster, unless otherwise stated.

Please report any issues via comments !

  1. Firsly, follow my earlier post on how to setup your own python virtual environment on UPPMAX.
  2. Once you have a prompt similar to: (devel) hostname ~$, you can continue, else, jump to 1.
  3. pip install drmaa Mercurial PyYAML
  4. Add the following env variables to your .bashrc:
    export DRMAA_LIBRARY_PATH=/bubo/sw/apps/build/slurm-drmaa/lib/libdrmaa.so
    export DRMAA_PATH=$DRMAA_LIBRARY_PATH
    

</pre>

  1. Create a file ~/.slurm_drmaa.conf with the contents:
    job_categories: {
      default: "-A <your project_account> -p devel"
    }
    

</pre>

  1. hg clone http://bitbucket.org/brainstorm/galaxy-central
  2. Edit universe_wsgi.ini from the provided sample so that it contains:
    admin_users = <your_admin_user>@example.com
    enable_api = True
    start_job_runners = drmaa
    default_cluster_job_runner = drmaa://-A <your project_account> -p devel
    

</pre>

  1. On your local machine: *ssh -f @ -L 8080:localhost:8080 -N*
  2. On your local machine: Fire up your browser and connect to http://localhost:8080

As a betatester you may expect some issues when running galaxy in that way. Firstly, keep in mind that it’ll not perform as fast as a production-quality setup, it’s just a developer instance. Furthermore the node you’re in might have time limit restrictions, meaning that your instance will be killed in 30 minutes if you don’t reserve a slot beforehand as Martin recommended on the section “Run galaxy on a node”.

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