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
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
line 13, in ?
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.
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