Getting syntax error on Join + environment_setup_file not read
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 *
On Jul 28, 2012, at 8:09 PM, Peter Schmitt wrote:
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
Hi Pete, It looks like the version of Python your tools are running is 2.4. Please make sure that `python` as executed on the cluster is >= 2.5.
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.
environment_setup_file is not applied to the Galaxy server, it's sourced in the environment in which tools are run. Anything that needs to be set in the environment for Galaxy itself to run should be done elsewhere, such as run.sh, ~/.profile, etc. --nate
--
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 <Mail Attachment.jpeg> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Nate Coraor -
Peter Schmitt