Re: [galaxy-user] Galaxy-Condor Permission Denied
Dear Nathan, We found that condor was running the job as the "nobody" user, which had no permissions to the files galaxy created in the database/pbs directory. This was fixed by setting TRUST_UID_DOMAIN = True in the condor config file. Now the job runs, but fails immediately because it cannot find the PATH environment variable. If I run the generated database/pbs/galaxy_.sh file manually at the command line, it works fine. Do we need any some environment setting in galaxy/condor? Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/stats/column_maker.py", line 7, in from galaxy.tools import validation File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 15, in from galaxy import util, jobs, model File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 4, in from galaxy import util, model File "/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 13, in import galaxy.datatypes.registry File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 6, in import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, wsf File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/data.py", line 7, in import metadata File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py", line 5, in from galaxy.web import form_builder File "/home/galaxy/galaxy-dist/lib/galaxy/web/__init__.py", line 5, in from framework import expose, json, json_pretty, require_login, require_admin, url_for, error, form, FormBuilder, expose_api File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 18, in import helpers File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py", line 4, in from webhelpers import * File "/home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/__init__.py", line 1, in from webhelpers.rails import * File "/home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/rails/__init__.py", line 9, in from text import * File "/home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/rails/text.py", line 10, in import webhelpers.textile as textile File "/home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/textile.py", line 241, in import tidy File "/usr/lib/pymodules/python2.6/tidy/__init__.py", line 43, in from tidy.lib import parse, parseString File "/usr/lib/pymodules/python2.6/tidy/lib.py", line 24, in os.environ['PATH'] = "%s%s%s" % (packagedir, os.pathsep, os.environ['PATH']) File "/usr/lib/python2.6/UserDict.py", line 22, in __getitem__ raise KeyError(key) KeyError: 'PATH' Thank you so much again for your help. Oren ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Galaxy-Condor Permission Denied
On Wed, Oct 05, 2011 at 01:00:35PM -0500, Oren Livne wrote: > Dear Nathan, > > We found that condor was running the job as the "nobody" user, which > had no permissions to the files galaxy created in the database/pbs > directory. This was fixed by setting > > TRUST_UID_DOMAIN = True > > in the condor config file. > > Now the job runs, but fails immediately because it cannot find the > PATH environment variable. If I run the generated > database/pbs/galaxy_.sh file manually at the command line, it > works fine. Do we need any some environment setting in > galaxy/condor? You can set the environment by using an "environment = " command in the submit file or, if appropriate, you can copy your environment to the job by inserting "getenv = true" in the submit file. This is described in the condor manual at http://www.cs.wisc.edu/condor/manual/v7.7/2_5Submitting_Job.html#2516 > Thank you so much again for your help. You're welcome Nathan Panike ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Galaxy-Condor Permission Denied
Dear Nick, Haven't heard back yet from condor, I found in previous posts and condor docs that this might have to do with the condor UID_DOMAIN config variable, which is set to $(FULL_HOSTNAME) in my case, as recommended therein. Also, "condor_master" is being run as root. Which user does condor believe you to be? The user running the "condor_submit" command is "galaxy", which has permissions to write that output file. But I don't know if this is the relevant uid or if condor is trying to open that file as a different user within the condor_submit command. Oren ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Galaxy-Condor Permission Denied
Dear Nathan, Thank you so much for your help. condor@vm-debian:/home/galaxy/galaxy-dist/database/pbs$ condor_q -- Submitter: vm-debian.uchad.uchospitals.edu : <165.68.219.43:56855> : vm-debian.uchad.uchospitals.edu ID OWNERSUBMITTED RUN_TIME ST PRI SIZE CMD 18.0 galaxy 10/5 12:01 0+00:00:01 H 0 0.0 galaxy_31.sh 1 jobs; 0 idle, 0 running, 1 held condor@vm-debian:/home/galaxy/galaxy-dist/database/pbs$ condor_q -f '%s\n' FileSystemDomain 18.0 uchad.uchospitals.edu condor@vm-debian:/home/galaxy/galaxy-dist/database/pbs$ condor_q -f '%s\n' Owner 18.0 galaxy condor@vm-debian:/home/galaxy/galaxy-dist/database/pbs$ condor_q -f '%s\n' User 18.0 gal...@uchad.uchospitals.edu We added the condor to the galaxy user group, but that didn't help. Oren ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Galaxy-Condor Permission Denied
On Wed, Oct 05, 2011 at 11:11:58AM -0500, Oren Livne wrote: > Dear Nick, > > Haven't heard back yet from condor, I found in previous posts and > condor docs that this might have to do with the condor UID_DOMAIN > config variable, which is set to $(FULL_HOSTNAME) in my case, as > recommended therein. Also, "condor_master" is being run as root. > >Which user does condor believe you to be? > The user running the "condor_submit" command is "galaxy", which has > permissions to write that output file. But I don't know if this is > the relevant uid or if condor is trying to open that file as a > different user within the condor_submit command. What is the output of the following? condor_q -f '%s\n' FileSystemDomain condor_q -f '%s\n' Owner condor_q -f '%s\n' User Nathan Panike ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Galaxy-Condor Permission Denied
You might want to ask about this on condor-us...@cs.wisc.edu, if it is a Condor problem. (cc'd) On Tue, Oct 04, 2011 at 04:53:24PM -0500, Oren Livne wrote: > Dear All, > > I am using Galaxy with condor as the scheduler via the DRMAA Job > Runner. on Debian 6. Jobs are submitted to COndor but they are held > because of permissions: > > condor@vm-debian:~$ condor_q -analyze 10.0 > > -- Submitter: vm-debian.uchad.uchospitals.edu : > <165.68.219.43:40312> : vm-debian.uchad.uchospitals.edu > --- > 010.000: Request is held. > > Hold reason: Error from vm-debian.uchad.uchospitals.edu: Failed to > open '/home/galaxy/galaxy-dist/database/pbs/19.o' as standard > output: Permission denied (errno 13) > > condor@vm-debian:~$ ls -l /home/galaxy/galaxy-dist/database/pbs/19.o > -rw-r--r-- 1 galaxy galaxy 0 Oct 4 16:40 > /home/galaxy/galaxy-dist/database/pbs/19.o > > I am running galaxy as the galaxy user. I also have a condor user. > How to ensure that jobs are submitted as the proper user? Which user does condor believe you to be? > Thanks so much, > Oren ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
