Hi, I try to run a local galaxy installation with a sge job runner. But whenever I start run.sh I get an Traceback (most recent call last): File "/data/bioinformatics/galaxy/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/data/bioinformatics/galaxy/lib/galaxy/app.py", line 64, in __init__ self.job_manager = jobs.JobManager( self ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 33, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 636, in __init__ import runners.sge File "/data/bioinformatics/galaxy/lib/galaxy/jobs/runners/sge.py", line 10, in <module> pkg_resources.require( "DRMAA_python" ) File "/data/bioinformatics/galaxy/lib/galaxy/eggs/__init__.py", line 558, in require if not egg.fetch(): File "/data/bioinformatics/galaxy/lib/galaxy/eggs/__init__.py", line 101, in fetch raise EggNotFetchable( self.name ) EggNotFetchable: DRMAA_python some nodes: drmaa_python is installed and can be used by the galaxy user (if SGE_ROOT and LD_LIBRARY_PATH are set) I first used python2.6 and fell back to 2.5 but the problems stays the same. Any idea how to proceed? regards, Andreas
Some additional info: I use the "Unified method", galaxy install directory is available from galaxy server and cluster nodes. Then I added start_job_runners=sge to universe_wsgi.ini Andreas PS: I just found that pkg_resources.require("drmaa") does not throw an exception.
I try to run a local galaxy installation with a sge job runner. But whenever I start run.sh I get an
Traceback (most recent call last): File "/data/bioinformatics/galaxy/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/data/bioinformatics/galaxy/lib/galaxy/app.py", line 64, in __init__ self.job_manager = jobs.JobManager( self ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 33, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 636, in __init__ import runners.sge File "/data/bioinformatics/galaxy/lib/galaxy/jobs/runners/sge.py", line 10, in <module> pkg_resources.require( "DRMAA_python" ) File "/data/bioinformatics/galaxy/lib/galaxy/eggs/__init__.py", line 558, in require if not egg.fetch(): File "/data/bioinformatics/galaxy/lib/galaxy/eggs/__init__.py", line 101, in fetch raise EggNotFetchable( self.name ) EggNotFetchable: DRMAA_python
some nodes:
drmaa_python is installed and can be used by the galaxy user (if SGE_ROOT and LD_LIBRARY_PATH are set) I first used python2.6 and fell back to 2.5 but the problems stays the same.
Any idea how to proceed?
regards, Andreas
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Hi,
I use the "Unified method", galaxy install directory is available from galaxy server and cluster nodes. Then I added start_job_runners=sge to universe_wsgi.ini
Andreas
PS: I just found that pkg_resources.require("drmaa") does not throw an exception.
but starting still does not work. I get an Traceback (most recent call last): File "/data/bioinformatics/galaxy/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/data/bioinformatics/galaxy/lib/galaxy/app.py", line 64, in __init__ self.job_manager = jobs.JobManager( self ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 33, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 636, in __init__ import runners.sge File "/data/bioinformatics/galaxy/lib/galaxy/jobs/runners/sge.py", line 22, in <module> DRMAA.Session.UNDETERMINED: 'process status cannot be determined', AttributeError: type object 'Session' has no attribute 'UNDETERMINED' So what version of drmaa_python do I need? I installed the latest available (drmaa-0.4a2-r17) BTW. I also have to remove the -S from the python invocation of run.sh to get this far. Otherwise the drmaa is not found again. Could that be because drmaa_python is in <PYTHONHOME>/site-packages ? Andreas
I try to run a local galaxy installation with a sge job runner. But whenever I start run.sh I get an
Traceback (most recent call last): File "/data/bioinformatics/galaxy/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/data/bioinformatics/galaxy/lib/galaxy/app.py", line 64, in __init__ self.job_manager = jobs.JobManager( self ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 33, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 636, in __init__ import runners.sge File "/data/bioinformatics/galaxy/lib/galaxy/jobs/runners/sge.py", line 10, in <module> pkg_resources.require( "DRMAA_python" ) File "/data/bioinformatics/galaxy/lib/galaxy/eggs/__init__.py", line 558, in require if not egg.fetch(): File "/data/bioinformatics/galaxy/lib/galaxy/eggs/__init__.py", line 101, in fetch raise EggNotFetchable( self.name ) EggNotFetchable: DRMAA_python
some nodes:
drmaa_python is installed and can be used by the galaxy user (if SGE_ROOT and LD_LIBRARY_PATH are set) I first used python2.6 and fell back to 2.5 but the problems stays the same.
Any idea how to proceed?
regards, Andreas
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Hi Andreas, The configuration instructions here: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster include a bit on how to build a DRMAA_python egg. I don't think DRMAA_python uses setuptools (and therefore doesn't create egg info) by default, so Galaxy still won't be able to 'require' it if not built using our method. Essentially: SGE_ROOT=/path/to/sge python scripts/scramble.py DRMAA_python And then add -S back to the python invocation in run.sh. You may also want to remove DRMAA_python from your site-packages. --nate Andreas Kuntzagk wrote:
Hi,
I use the "Unified method", galaxy install directory is available from galaxy server and cluster nodes. Then I added start_job_runners=sge to universe_wsgi.ini
Andreas
PS: I just found that pkg_resources.require("drmaa") does not throw an exception.
but starting still does not work. I get an Traceback (most recent call last): File "/data/bioinformatics/galaxy/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/data/bioinformatics/galaxy/lib/galaxy/app.py", line 64, in __init__ self.job_manager = jobs.JobManager( self ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 33, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 636, in __init__ import runners.sge File "/data/bioinformatics/galaxy/lib/galaxy/jobs/runners/sge.py", line 22, in <module> DRMAA.Session.UNDETERMINED: 'process status cannot be determined', AttributeError: type object 'Session' has no attribute 'UNDETERMINED'
So what version of drmaa_python do I need? I installed the latest available (drmaa-0.4a2-r17)
BTW. I also have to remove the -S from the python invocation of run.sh to get this far. Otherwise the drmaa is not found again. Could that be because drmaa_python is in <PYTHONHOME>/site-packages ?
Andreas
I try to run a local galaxy installation with a sge job runner. But whenever I start run.sh I get an
Traceback (most recent call last): File "/data/bioinformatics/galaxy/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/data/bioinformatics/galaxy/lib/galaxy/app.py", line 64, in __init__ self.job_manager = jobs.JobManager( self ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 33, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 636, in __init__ import runners.sge File "/data/bioinformatics/galaxy/lib/galaxy/jobs/runners/sge.py", line 10, in <module> pkg_resources.require( "DRMAA_python" ) File "/data/bioinformatics/galaxy/lib/galaxy/eggs/__init__.py", line 558, in require if not egg.fetch(): File "/data/bioinformatics/galaxy/lib/galaxy/eggs/__init__.py", line 101, in fetch raise EggNotFetchable( self.name ) EggNotFetchable: DRMAA_python
some nodes:
drmaa_python is installed and can be used by the galaxy user (if SGE_ROOT and LD_LIBRARY_PATH are set) I first used python2.6 and fell back to 2.5 but the problems stays the same.
Any idea how to proceed?
regards, Andreas
_______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
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participants (2)
-
Andreas Kuntzagk -
Nate Coraor