To give this question better visibility, I am going to move it over to the galaxy-dev@bx.psu.edu mailing list. Thanks! Jen Galaxy team fwd from galaxy-user On 7/17/12 11:31 AM, Scott McManus wrote:

Hi Kevin-

That's truly odd. The error happens when the offending file is imported, which means that it is a syntax issue that should have been seen earlier. I'll take a look at this soon (unless someone else beats me to it).

In the meantime, of course, do not use the use_tasked_jobs on this instance of Galaxy. If others have seen similar issues, then please speak up.

-Scott

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Hi,

I am using Python 2.7. I am running with an hg checked out, up to date version of "https://bitbucket.org/galaxy/galaxy-dist/".

I am very new to Galaxy. I have an instance setup *and running* locally. I am able to perform routine actions such as uploading files, processing with Picard, and aligning with BWA. I have been able to make the jobs execute out our SGE cluster.

In order to better utilize my cluster, I attempted to enable parallelism of the tasks that support it (such as BWA) by configuring the *universe_wsgi.ini* file with the parameter

use_tasked_jobs = True

When I do this and attempt execute a BWA alignment on a 4.1Gb fastq file, I am given the error

Result 256 from mv /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_1/dataset_21.dat /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/files/000/dataset_21.dat /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 25, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/datatypes/registry.py", line 146 finally: ^ SyntaxError: invalid syntax The alignment failed.

If you need the complete error message, contact me and I can supply you with it. It's too large to paste in-line and attachments aren't allowed.

Is there more I need to do to enable parallel jobs (splitting of input, align, then merge)?

Any suggestions are greatly appreciated.

Kevin

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___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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-- Jennifer Jackson http://galaxyproject.org