Ryan Golhar wrote: > I've configured my local instance of galaxy to run with drmaa. > Unfortunately, there is a problem that after some time, galaxy loses > its ability to talk to Torque, hence Galaxy thinks long-running jobs > have failed and its unable to submit new jobs. > > I have no idea how this stuff works underneath so I thought I'd try > setting up pbs_python instead, but I get an error when I run the > command given onthe Config/Cluster Wiki > > (galaxy_env)[galaxy@genomes galaxy-dist]$ > LIBTORQUE=/campus/apps/amd64_linux26/packages/torque-2.4.8/lib/libtorque.so > python scripts/scramble.py pbs_python
This one should be: $ LIBTORQUE_DIR=/campus/apps/amd64_linux26/packages/torque-2.4.8/lib python scripts/scramble.py pbs_python > fetch_one(): Using existing source, remove to download again: > > /home/galaxy/galaxy-dist/scripts/scramble/archives/pbs_python-4.1.0.tar.gz > unpack_source(): Removing old build directory at: > > /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python > unpack_source(): Unpacked to: > > /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python > copy_build_script(): Using build script > /home/galaxy/galaxy-dist/scripts/scramble/scripts/pbs_python.py > run_scramble_script(): Beginning build > run_scramble_script(): Executing in > /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python: > /home/galaxy/galaxy_env/bin/python -ES scramble.py > Traceback (most recent call last): > File "scramble.py", line 1, in <module> > import os, sys, shutil > ImportError: No module named shutil > Traceback (most recent call last): > File "scripts/scramble.py", line 44, in <module> > egg.scramble() > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line > 58, in scramble > self.run_scramble_script() > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line > 207, in run_scramble_script > raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" > % ( sys._getframe().f_code.co_name, self.name, self.version ) ) > galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg > build failed for pbs_python 4.1.0 > (galaxy_env)[galaxy@genomes galaxy-dist]$ > > It looks like it can't find shutil. I'm also running under a > virtualenv as indicated by the ProductionServer wiki page, and not > sure this makes a difference or not. Does anyone know how to > correct this? This is a conflict between virtualenv and the '-S' option to Python. I have just committed a fix for this, and it will be available in our stable distribution soon. In the meantime, you can work around this with: $ cd /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python $ LIBTORQUE_DIR=/campus/apps/amd64_linux26/packages/torque-2.4.8/lib /home/galaxy/galaxy_env/bin/python scramble.py $ cp dist/pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg /home/galaxy/galaxy-dist/eggs --nate > > > > _______________________________________________ > To manage your subscriptions to this and other Galaxy lists, please use the > interface at: > > http://lists.bx.psu.edu/ _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
