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