August 2015 - galaxy-dev - lists.galaxyproject.org

collection in workflow fail
by Alexander Vowinkel 03 Aug '15

03 Aug '15

Hi, I'm running cutadapt (from TS) on a collection with 96 datasets, started from a workflow as an intermediate step. About half of them fail with this message. Traceback (most recent call last): File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/runners/__init__.py", line 590, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/__init__.py", line 1261, in finish ActionBox.execute(self.app, self.sa_session, pja.post_job_action, job) File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/actions/post.py", line 532, in execute ActionBox.actions[pja.action_type].execute(app, sa_session, pja, job, replacement_dict) File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/actions/post.py", line 405, in execute for input_dataset in [x.dataset for x in j2c.input_datasets if x.dataset.creating_job.workflow_invocation_step and x.dataset.creating_job.workflow_invocation_step.workflow_invocation == wfi]: AttributeError: 'NoneType' object has no attribute 'input_datasets' Running release 15.07 rev cf29f6c4a7 <https://github.com/galaxyproject/galaxy/commit/cf29f6c4a77a084bcf4732ddf1c5…> Is that Known? How to avoid? Best, Alexander

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Call for Tool Shed Admins
by Martin Čech 03 Aug '15

03 Aug '15

Hi everybody, similar to the existing mailing list of Galaxy instance admins we are putting together a mailing list of admins of Tool Shed instances (especially the public ones) so if you administer one (or more) please respond to me privately and I will put you on it. Thank you very much. Martin, Galaxy Team

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migrated_tools_conf.xml propose
by Mic 03 Aug '15

03 Aug '15

Hello, I found this ( https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/8d1fe99e… ) file. If I would copy migrated_tools_conf.xml into the galaxy/config folder then would galaxy/run.sh script install all tools describe in that file? Thank you in advance. Mic

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configuring job runner slurm on cloudman
by Alexander Vowinkel 31 Jul '15

31 Jul '15

Hi, I have adopted /mnt/galaxy/galaxy-app/config/job_conf.xml: I added a destination with following param: <param id="nativeSpecification">-N1 --cpus-per-task 1 --mem-per-cpu=4G</param> Galaxy service was restarted after chaning this. Now I get the error "Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator." when I try to run a job. Looking in the log gives: galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493) submitting file /mnt/galaxy/tmp/job_working_directory/000/493/galaxy_493.sh > galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493) native specification is: -N1 --cpus-per-task 1 --mem-per-cpu=4G > galaxy.jobs.runners.drmaa ERROR 2015-07-06 22:50:40,187 (493) drmaa.Session.runJob() failed unconditionally > Traceback (most recent call last): > [...] > InvalidAttributeValueException: code 14: Invalid native specification: -N1 --cpus-per-task 1 --mem-per-cpu=4G Well. running this as galaxy user in the console with $ srun -N1 --cpus-per-task 1 --mem-per-cpu=4G > /mnt/galaxy/tmp/job_working_directory/000/494/galaxy_494.sh , it actually runs good. I was wondering if this is connected with the fact that the log states " galaxy.jobs.runners.drmaa" and not something like galaxy.jobs.runners.slurm, like defined in the job_conf.xml: <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> So - What is going wrong here? Am I working on the wrong job_conf.xml? What does galaxy do here? Thanks for help!Alexander

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