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September 2019

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pbs-python issues
by Sandra Maksimovic 11 Oct '19

11 Oct '19

Hi all, As a galaxy newbie, I'm struggling to get the pbs-python module working on our galaxy instance. PBS is installed to a custom location on a shared filesystem mounted via NFS to our galaxy server, however, installing pbs-python using the git clone / python venv method in the documentation fails because it can't find PBS and there does not appear to be any way to define it for pbs-python (I could be wrong?). ... gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 … [View More]-fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DTORQUE_4 -I/usr/include/torque -Isrc/C++ -I/usr/include/python2.7 -c src/C++/pbs_wrap.cxx -o build/temp.linux-x86_64-2.7/src/C++/pbs_wrap.o In file included from src/C++/pbs_wrap.cxx:2978:0: src/C++/pbs_ifl.h:90:32: fatal error: u_hash_map_structs.h: No such file or directory #include "u_hash_map_structs.h" ^ compilation terminated. error: command 'gcc' failed with exit status 1 So I went ahead and installed pbs_python from source (which does allow you define a PBS_PYTHON_INCLUDEDIR environment variable), however, galaxy does not seem to like this as evidenced by errors during startup. I suspect this has to do with pbs_python not being installed into the galaxy virtual environment. galaxy[97486]: Traceback (most recent call last): galaxy[97486]: File "<string>", line 1, in <module> galaxy[97486]: File "/hpc/software/installed/galaxy/19.05/lib/galaxy/dependencies/__init__.py", line 179, in optional galaxy[97486]: conditional = ConditionalDependencies(config_file) galaxy[97486]: File "/hpc/software/installed/galaxy/19.05/lib/galaxy/dependencies/__init__.py", line 32, in __init__ galaxy[97486]: self.parse_configs() galaxy[97486]: File "/hpc/software/installed/galaxy/19.05/lib/galaxy/dependencies/__init__.py", line 41, in parse_configs galaxy[97486]: for plugin in ElementTree.parse(job_conf_xml).find('plugins').findall('plugin'): galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182, in parse galaxy[97486]: tree.parse(source, parser) galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse galaxy[97486]: parser.feed(data) galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed galaxy[97486]: self._raiseerror(v) galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror galaxy[97486]: raise err galaxy[97486]: xml.etree.ElementTree.ParseError: junk after document element: line 4, column 0 I've attempted reinstalls of the git clone / python venv method with the PBS environment variable to no avail. I was wondering if someone might have any ideas about working around this roadblock, or may have encountered a similar module installation issue in the past? Also, I was hoping to get some ideas/examples of generic job_conf.xml definitions for PBS clusters? Things like best practices, caveats, etc. My understanding is that, unless configured otherwise, galaxy will submit jobs as the galaxy user and that configuring the server to run jobs as end users themselves is difficult/risky. Just wondering if you guys might have opinions/thoughts/recommendations about this? And finally, what would be a good way to test that galaxy is submitting jobs to the queue properly? Is there some generic test data/procedure to verify that the galaxy instance is working as expected? Thanks, Sandra Maksimovic Systems Administrator Information Technology Murdoch Children's Research Institute The Royal Children's Hospital, 50 Flemington Road Parkville, Victoria 3052 Australia T +61 3 8341 6498 E sandra.maksimovic(a)mcri.edu.au<mailto:sandra.maksimovic@mcri.edu.au> W mcri.edu.au<https://www.mcri.edu.au/> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. [View Less]

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