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>
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