On Dec 18, 2012, at 12:05 PM, "Ganote, Carrie L" <cganote@iu.edu> wrote:

Hi all,

Right now I have drmaa running with Torque. I have a virtual machine with Galaxy installed on it, a filesystem mounted on the virtual machine that holds the dataset info, and a cluster that runs big jobs and also has access to the mounted filesystem. When running Galaxy as a real user, I get an error because the real user has no pwd listing in the virtual machine. In this entry there is mention of galaxy_user.username; where is that and how is it populated? I use kerberos to authenticate through apache.

Any clues appreciated!

Here's the dump: galaxy.jobs ERROR 2012-12-18 11:29:01,871 (989) Failed to change ownership of /Filesystem/job_working_directory/000/989, making world-writable instead Traceback (most recent call last): File "/Prefix/galaxy-dist/lib/galaxy/jobs/__init__.py", line 893, in change_ownership_for_run self._change_ownership( self.user_system_pwent[0], str( self.user_system_pwent[3] ) ) TypeError: 'NoneType' object is unsubscriptable galaxy.jobs.runners.drmaa ERROR 2012-12-18 11:29:01,928 Uncaught exception queueing job Traceback (most recent call last): File "/Prefix/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 145, in run_next self.queue_job( obj ) File "/Prefix/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 237, in queue_job log.debug( '(%s) submitting with credentials: %s [uid: %s]' % ( galaxy_id_tag, job_wrapper.user_system_pwent[0], job_wrapper.user_system_pwent[2] ) ) TypeError: 'NoneType' object is unsubscriptable

Carrie Ganote

Hi Carrie, I run a crontab job every 5 minutes that repopulates the galaxy database with the real user names we use instead of the email style user names by updating the galaxy_user.username column. Then, I patch jobs/__init__.py as follows: # self.__user_system_pwent = pwd.getpwnam( job.user.email.split('@')[0] ) self.__user_system_pwent = pwd.getpwnam( job.user.username ) Regards, Alex