Re: [galaxy-dev] Galaxy users on virtual machine
On Dec 18, 2012, at 12:05 PM, Ganote, Carrie L cgan...@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
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Re: [galaxy-dev] Galaxy users on virtual machine
Hi Alex,
I see what you are saying, but I think our situations are slightly different.
The line
self.__user_system_pwent =
pwd.getpwnam(job.user.email.split('@')[0] )
*does* return the correct username, however, that user is not present in the
Virtual machine that is running Galaxy, so when the job runner calls for
pwd.getpwuid(), there is nothing there. By the way, the VM uses key
authentication only, not passwords.
The problem I think I'm having is that the /etc/passwd file I want to use is
located on the cluster, not on the virtual machine. I'm not sure if I can just
copy that file over. How else can I get ahold of the uid of the user who
cannot log in to the machine Galaxy is running on?
Thanks for the help,
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
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Galaxy users on virtual machine
We're using ldap authentication on our cluster, so our /etc/passwd files don't
have any user data and the credentials are returned by ldap. You will have to
adjust this to your situation. You can rsync /etc/passwd from elsewhere or
fiddle with PAM to work something out for your key-based setup. Sorry, I don't
have more insight into that part.
Regards,
Alex
On Dec 18, 2012, at 2:27 PM, cgan...@iu.edu wrote:
Hi Alex,
I see what you are saying, but I think our situations are slightly different.
The line
self.__user_system_pwent =
pwd.getpwnam(job.user.email.split('@')[0] )
*does* return the correct username, however, that user is not present in the
Virtual machine that is running Galaxy, so when the job runner calls for
pwd.getpwuid(), there is nothing there. By the way, the VM uses key
authentication only, not passwords.
The problem I think I'm having is that the /etc/passwd file I want to use is
located on the cluster, not on the virtual machine. I'm not sure if I can
just copy that file over. How else can I get ahold of the uid of the user
who cannot log in to the machine Galaxy is running on?
Thanks for the help,
Carrie Ganote
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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