[galaxy-dev] Attempting to use parallelism in BWA

17 Jul 2012

      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/
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Jennifer Jackson
http://galaxyproject.org