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
- Original Message -
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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