Hi everybody,
I managed to configure Galaxy to work with DRMAA in our cluster but after the job finished, the dataset state is set to error. Here is the last few lines of the paster.log file:
galaxy.jobs.runners.drmaa DEBUG 2014-01-27 10:52:50,449 (181) submitting with credentials: jing [uid: 3663]
galaxy.jobs.runners.drmaa DEBUG 2014-01-27 10:52:50,490 (181) Job script for external submission is: /work/galaxy/galaxy/galaxy-dist/database/pbs/181.jt_json
galaxy.jobs.runners.drmaa INFO 2014-01-27 10:52:51,175 (181) queued as 961147
galaxy.jobs DEBUG 2014-01-27 10:52:51,225 (181) Persisting job destination (destination id: drmaa)
galaxy.jobs.runners.drmaa DEBUG 2014-01-27 10:52:51,781 (181/961147) state change: job is running
galaxy.jobs.runners.drmaa DEBUG 2014-01-27 10:52:56,004 (181/961147) state change: job finished normally
galaxy.jobs DEBUG 2014-01-27 10:52:56,276 (181) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /work/galaxy/galaxy/galaxy-dist/database/job_working_directory/000/181 galaxy 11295
galaxy.jobs DEBUG 2014-01-27 10:52:57,161 (181) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /work/galaxy/galaxy/galaxy-dist/database/job_working_directory/000/181 galaxy 11295
galaxy.jobs DEBUG 2014-01-27 10:52:59,777 setting dataset state to ERROR
galaxy.jobs DEBUG 2014-01-27 10:52:59,871 job 181 ended
In the browser, the stderr file says:
Traceback (most recent call last):
File "/work/galaxy/galaxy/galaxy-dist/tools/data_source/data_source.py", line 6, in <module>
from galaxy.util.json import from_json_string, to_json_string
File "/work/galaxy/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 14, in <module>
pkg_resources.require( 'docutils' )
File "/work/galaxy/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 414, in require
raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
galaxy.eggs.EggNotFetchable: ['docutils']
Traceback (most recent call last):
File "./scripts/set_metadata.py", line 29, in <module>
import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers
File "/work/galaxy/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 10, in <module>
eggs.require("pexpect")
File "/work/galaxy/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 414, in require
raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
galaxy.eggs.EggNotFetchable: ['pexpect']
The "docutils" and "pexpect"
eggs are in the /work/galaxy/galaxy/galaxy-dist/eggs folder and I don't see why they are not fetchable. Any help is appreciated. Thanks.
-Jing