Hello,
I've been trying hard for past week or so to queue jobs via PBS to run our ATAC sequence in galaxy. I'm able successfully run a sequence without modifying the job_conf.xml file. i.e. running the analysis locally on the default server. However if I modify the job_conf.xml to use pbs, I couldnt start galaxy and it gives me bunch of errors.
Here is my modified job_conf.xml file -
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<job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" worker="8"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="batch"> <destination id="local" runner="local"/> <destination id="batch" runner="pbs" >="" <param="" id="Resource_List">-l nodes=1:ppn=8,walltime=72:00:00</param> <param id="-p">128</param> </destination> </destinations> </job_conf>
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and here is my error when I start galaxy(>> sh run.sh) just the last few lines.. .. .. galaxy.jobs DEBUG 2016-06-30 17:47:56,375 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' Traceback (most recent call last): File "/home/lakshmananbm/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 63, in paste_app_factory app = galaxy.app.UniverseApplication( global_conf=global_conf, *kwargs ) File "/home/lakshmananbm/galaxy/lib/galaxy/app.py", line 174, in __init__ self.job_manager = manager.JobManager( self ) File "/home/lakshmananbm/galaxy/lib/galaxy/jobs/manager.py", line 23, in __init__ self.job_handler = handler.JobHandler( app ) File "/home/lakshmananbm/galaxy/lib/galaxy/jobs/handler.py", line 32, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/home/lakshmananbm/galaxy/lib/galaxy/jobs/handler.py", line 723, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/home/lakshmananbm/galaxy/lib/galaxy/jobs/__init__.py", line 672, in get_job_runner_plugins rval[id] = runner_class( self.app, runner[ 'workers' ], *runner.get( 'kwds', {} ) ) File "/home/lakshmananbm/galaxy/lib/galaxy/jobs/runners/pbs.py", line 93, in __init__ assert pbs is not None, PBS_IMPORT_MESSAGE AssertionError: The Python pbs-python package is required to use this feature, please install it or correct the following error: ImportError /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ~/galaxy/.venv/lib/python2.7/site-packages/pbs/_pbs.so)
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I hope somebody could help me debug this issue.
PS. while going though forum, it mentioned about editing eggs.ini file. But I dont see that file in my galaxy folder, maybe because I'm using newer version? Also I do not have root permission but not sure if that is related to my error.
THanks!! Bala
