I installed bismark from the toolshed (bgruening) with all dependencies having been installed successfully and I generated the genomes according to the instructions.
While trying to test the tool I got the following error.
galaxy.jobs.handler ERROR 2013-09-04 13:14:26,267 Failed to generate job destination
Traceback (most recent call last):
File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 287, in __check_if_ready_to_run
self.job_wrappers[
job.id].job_destination
File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 617, in job_destination
return self.job_runner_mapper.get_job_destination(self.params)
File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 163, in get_job_destination
self.__cache_job_destination( params )
File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 148, in __cache_job_destination
raw_job_destination = self.job_wrapper.tool.get_job_destination( params )
AttributeError: 'NoneType' object has no attribute 'get_job_destination'
galaxy.datatypes.metadata DEBUG 2013-09-04 13:14:26,905 Cleaning up external metadata files
galaxy.jobs.handler ERROR 2013-09-04 13:14:27,034 (1316) Error checking job readiness
I'm using the old style job configuration (the one in universe_wsgi.ini). Could that be the issue?