[galaxy-dev] Attempting to use parallelism in BWA

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

---

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:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/