Hi Ulf, you can set a virtualenv to be used in your job_conf.xml file. The following line would go into the `<destination></destination>` tag: `<env file="path_to_venv/bin/activate" />`
Best, Marius On 25 October 2017 at 16:56, Ulf Schaefer <[email protected]> wrote: > Hi again > > Update, sorry for spamming: > > It is not ALL jobs that fail. Only the ones that get dispatched to our > Grid Engine cluster (so nearly all). > > The reason appears to be that the path to the Python binary is added to > the PATH variable when the job arrives on the worker node: > > [galaxy_hpc@hpc1node25 galaxy-dist]$ export PATH=/home/galaxy_hpc/galaxy-d > ist/.venv/bin:/tmp/5000354.1.researchmid.q:/usr/local/bin:/bin:/usr/bin > [galaxy_hpc@hpc1node25 galaxy-dist]$ python > Could not find platform dependent libraries <exec_prefix> > Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] > Python 2.7.6 (default, Oct 25 2017, 12:28:23) > [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> import json > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > ImportError: No module named json > > This is the wrong python to be running there. It should just go with the > one in /usr/bin. If I change PATH, it works fine: > > [galaxy_hpc@hpc1node25 galaxy-dist]$ export PATH=/tmp/5000354.1.researchmi > d.q:/usr/local/bin:/bin:/usr/bin[galaxy_hpc@hpc1node25 galaxy-dist]$ > python > Python 2.6.6 (r266:84292, Aug 9 2016, 06:11:56) > [GCC 4.4.7 20120313 (Red Hat 4.4.7-17)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> import json > >>> > > Does anyone have an idea how I can stop this from happening? Where is the > PATH set before submitting the job? > > Thanks > Ulf > > > > > > > On 25/10/17 15:23, Ulf Schaefer wrote: > >> Hi all >> >> After running the recommended update I am now on branch 17.09. As part >> of the update I set up a new virtual env running an additional python >> 2.7.6. My previous virtual env was running 2.6.6 which is a system >> requirement for Centos 6. >> >> All dependencies were installed and Galaxy starts fine, but no tools >> run. The error is always a variation of this: >> >> Could not find platform dependent libraries <exec_prefix> >> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] >> Traceback (most recent call last): >> File >> "galaxy-dist/database/jobs_directory/000/418/418014/set_meta >> data_4LcsZv.py", >> line 1, in <module> >> from galaxy_ext.metadata.set_metadata import set_metadata; >> set_metadata() >> File "galaxy-dist/lib/galaxy_ext/metadata/set_metadata.py", line 19, >> in <module> >> import json >> ImportError: No module named json >> >> I put some debug output at the top of set_metadata.py and it is indeed >> running the correct python version from the virtual env. Needless to say >> I can import json just fine using that python version. Any ideas? >> >> Any help is greatly appreciated. >> >> Thanks >> Ulf >> >> > ************************************************************************** > The information contained in the EMail and any attachments is confidential > and intended solely and for the attention and use of the named > addressee(s). It may not be disclosed to any other person without the > express authority of Public Health England, or the intended recipient, or > both. If you are not the intended recipient, you must not disclose, copy, > distribute or retain this message or any part of it. This footnote also > confirms that this EMail has been swept for computer viruses by > Symantec.Cloud, but please re-sweep any attachments before opening or > saving. http://www.gov.uk/PHE > ************************************************************************** > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ >
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