# Galaxy on UPPMAX, simplified

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.

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


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


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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


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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”.