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?