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
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