Dear Galaxy Team,
I just updated my local instance of galaxy, and now I have a problem with the "DRMAA_python" egg, which makes it impossible to run jobs on our SGE cluster. I get the following error message after executing "run.sh":
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Traceback (most recent call last): File "/rahome/webservices/galaxy_test/lib/galaxy/jobs/__init__.py", line 1028, in _load_plugin module = __import__( module_name ) File "/rahome/webservices/galaxy_test/lib/galaxy/jobs/runners/sge.py", line 28, in <module> raise Exception( egg_message % str( e ) ) Exception:
The 'sge' runner depends on 'DRMAA_python' which is not installed. Galaxy's "scramble" system should make this installation simple, please follow the instructions found at:
http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
Additional errors may follow: ['DRMAA_python']
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I read the instructions and set the corresponding environment variable to tell galaxy about the location of the DRMAA library using the command:
export DRMAA_LIBRARY_PATH=/opt/sge-6.1/lib/lx24-x86/libdrmaa.so.1.0
When I started galaxy again, the same error message (see above) occurred. I also tried to scramble the DRMAA_python egg, which resulted in the following error message:
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fetch_one(): Using existing source, remove to download again:
/rahome/webservices/galaxy_test/scripts/scramble/archives/DRMAA_python-0.2.tar.gz unpack_source(): Removing old build directory at:
/rahome/webservices/galaxy_test/scripts/scramble/build/py2.6-linux-i686-ucs4/DRMAA_python unpack_source(): Unpacked to:
/rahome/webservices/galaxy_test/scripts/scramble/build/py2.6-linux-i686-ucs4/DRMAA_python copy_build_script(): Using build script /rahome/webservices/galaxy_test/scripts/scramble/scripts/DRMAA_python.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /rahome/webservices/galaxy_test/scripts/scramble/build/py2.6-linux-i686-ucs4/DRMAA_python: /usr/bin/python26 scramble.py main(): Patching setup.py running bdist_egg running egg_info creating DRMAA_python.egg-info writing DRMAA_python.egg-info/PKG-INFO writing top-level names to DRMAA_python.egg-info/top_level.txt writing dependency_links to DRMAA_python.egg-info/dependency_links.txt writing manifest file 'DRMAA_python.egg-info/SOURCES.txt' reading manifest file 'DRMAA_python.egg-info/SOURCES.txt' writing manifest file 'DRMAA_python.egg-info/SOURCES.txt' installing library code to build/bdist.linux-i686/egg running install_lib running build_py creating build creating build/lib.linux-i686-2.6 copying DRMAA.py -> build/lib.linux-i686-2.6 copying cDRMAA.py -> build/lib.linux-i686-2.6 running build_ext building '_cDRMAA' extension creating build/temp.linux-i686-2.6 gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind\ -tables -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/opt/sge-6.1/include -I/usr/include/python2.6 -c cDRMAA_wrap.c -o build/temp.linux-i686-2.6/cDRMAA_wrap.o -Wno-unused cDRMAA_wrap.c:13:20: error: Python.h: No such file or directory cDRMAA_wrap.c:358: error: expected specifier-qualifier-list before ‘PyObject’ cDRMAA_wrap.c:364: error: expected specifier-qualifier-list before ‘PyObject_HEAD’ ... error: command 'gcc' failed with exit status 1 Traceback (most recent call last): File "scripts/scramble.py", line 44, in <module> egg.scramble() File "/rahome/webservices/galaxy_test/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/rahome/webservices/galaxy_test/lib/galaxy/eggs/scramble.py", line 206, 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 DRMAA_python 0.2
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I would very much appreciate your help in fixing this problem.
Kind regards, Johannes