SLURM integration
Hello there I am working on getting galaxy to work with the slurm queuing system. I think i have solved the slurm part of the problem (submit, status, running etc), but some local problems still exist. Our site is using the modules system (http://modules.sourceforge.net/) to handle software, and there are some kinks to work out with that, but as far as i can see, the slurm is working. It is still a work in progress, but i think it could be useful for other people who are trying to do the same thing. All the adaptations are at the moment very specific for our site, but I hope to make it possible to integrate it with the vanilla galaxy. I have a short description of what i have done at this blog: https://www.uppnex.uu.se/blog/26/galaxy-uppmax A bitbucket for the code can be found here: https://bitbucket.org/dahlo/galaxy-central Best regards Martin Dahlö --- Bioinformatic support martin.dahlo@scilifelab.uu.se +46 18 611 59 59 +46 706 70 79 55 http://www.scilifelab.uu.se/ http://www.uppnex.uu.se ---
Hello Martin, Nice to see you over here :) I just managed to fix my own issues with the "module system" this morning, maybe it'll be useful for you: unset PYTHONHOME But that would probably require more work on your side (a.k.a, setting virtualenv): $ module list No Modulefiles Currently Loaded. mkdir -p $HOME/opt/mypython/lib/python2.6/site-packages easy_install-2.6 --prefix=~/opt/mypython pip pip install virtualenvwrapper --install-option="--prefix=~/opt/mypython" mkvirtualenv --python=python2.6 --no-site-packages galaxy_env That should create an isolated python environment for you, hopefully not affected by the environment pollution that the module system typically does. Again, good job with the SLURM integration ! ;) PD: Have a look at the message that appeared just after your's (Passing username to drmaa.py) ;) On 2011-06-15 13:16, Martin Dahlö wrote:
Hello there
I am working on getting galaxy to work with the slurm queuing system. I think i have solved the slurm part of the problem (submit, status, running etc), but some local problems still exist. Our site is using the modules system (http://modules.sourceforge.net/) to handle software, and there are some kinks to work out with that, but as far as i can see, the slurm is working.
It is still a work in progress, but i think it could be useful for other people who are trying to do the same thing. All the adaptations are at the moment very specific for our site, but I hope to make it possible to integrate it with the vanilla galaxy.
I have a short description of what i have done at this blog:
https://www.uppnex.uu.se/blog/26/galaxy-uppmax
A bitbucket for the code can be found here:
https://bitbucket.org/dahlo/galaxy-central
Best regards Martin Dahlö --- Bioinformatic support martin.dahlo@scilifelab.uu.se
+46 18 611 59 59 +46 706 70 79 55 http://www.scilifelab.uu.se/ http://www.uppnex.uu.se ---
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participants (2)
-
Martin Dahlö -
Roman Valls