Hi, we are trying to install a local version of Galaxy on a computing cluster using sge but there are a few issues with dependencies and setting paths. For instance we can get gsummary.py to run on the command line by manually setting PYTHONPATH to the RPy area, however within Galaxy the following error is returned: File "/exports/work/biology_cell_galaxy/galaxy/tools/stats/gsummary.py", line 4, in ? from rpy import * ImportError: No module named rpy Is there a preferred way to set the PYTHONPATH environment variable? I see references to it in setup_paths.sh, but I'm not sure when/if this gets run. It appears that the PYTHONPATH is ignored by setup.sh and by run.sh. run.sh calls python with environment disabled (-E). Even with -E removed the PYTHONPATH appears not to get through. The error is the same on the command line with PYTHONPATH undefined. It is clear the problem is getting Galaxy to respect the PYTHONPATH. Any help would be greatly appreciated. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Hi, What cluster management are you running. As I learned on this list for SGE you need to set the .sge_request of the galaxy user to set PYTHONPATH (and other environment staff. e.q. LD_LIBRARY_PATH for R libraries) regards, Andreas SHAUN WEBB wrote:
Hi, we are trying to install a local version of Galaxy on a computing cluster using sge but there are a few issues with dependencies and setting paths. For instance we can get gsummary.py to run on the command line by manually setting PYTHONPATH to the RPy area, however within Galaxy the following error is returned:
File "/exports/work/biology_cell_galaxy/galaxy/tools/stats/gsummary.py", line 4, in ? from rpy import * ImportError: No module named rpy
Is there a preferred way to set the PYTHONPATH environment variable? I see references to it in setup_paths.sh, but I'm not sure when/if this gets run. It appears that the PYTHONPATH is ignored by setup.sh and by run.sh. run.sh calls python with environment disabled (-E). Even with -E removed the PYTHONPATH appears not to get through.
The error is the same on the command line with PYTHONPATH undefined. It is clear the problem is getting Galaxy to respect the PYTHONPATH.
Any help would be greatly appreciated.
Thanks Shaun Webb
Andreas Kuntzagk wrote:
What cluster management are you running. As I learned on this list for SGE you need to set the .sge_request of the galaxy user to set PYTHONPATH (and other environment staff. e.q. LD_LIBRARY_PATH for R libraries)
Andreas is correct, you'll need to configure it in your user's environment. The Galaxy server itself starts with 'python -ES' to avoid conflicts, but when tools are run (either locally or on the node) they inherit the PYTHONPATH from the user's environment. In PBS we do this via the user's .profile, and the method Andreas uses works for SGE. --nate
participants (3)
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Andreas Kuntzagk -
Nate Coraor -
SHAUN WEBB