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
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?



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