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New galaxy install. Running the tutorial
Galaxy 101 and trying to do the join. Get the following error in
the stderr of the job: Traceback (most recent call last): File "/opt/galaxy/galaxy-dist/tools/new_operations/gops_join.py", line 20, in ? from galaxy.tools.util.galaxyops import * File "/opt/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 15, in ? from galaxy import util, jobs, model File "/opt/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 15, in ? from galaxy import util, model File "/opt/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/opt/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 146 finally: ^ SyntaxError: invalid syntax Traceback (most recent call last): File "./scripts/set_metadata.py", line 24, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/opt/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 146 finally: ^ SyntaxError: invalid syntax Also I believe the line, environment_setup_file = scripts/galaxy.sh, is not being used any longer. When I put the line: export DRMAA_LIBRARY_PATH=/opt/drmaa/1.0.12/lib/libdrmaa.so.1.0.12, in there the server didn't see it. When I added that line to the top of run.sh, it does. --
Pete Schmitt Technical Director: Discovery Cluster NH INBRE Grid Computational Genetics Lab Dartmouth College, HB 6223 L24 Berry/Baker Library Hanover, NH 03755 Phone: 603-646-8109 http://discovery.dartmouth.edu http://columbia.dartmouth.edu/grid http://www.epistasis.org  |
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