Re: [galaxy-dev] Problems with Galaxy cluster using grid engine
Hi John, Yes, I came across a listing to enable this in /config/galaxy.ini for Gridengine. Peter van Heusden brought this error to my attention. I have now commented this out and can now upload files. #drmaa_external_runjob_script = /share/apps/galaxy/scripts/drmaa_external_runner.py #drmaa_external_killjob_script = /share/apps/galaxy/scripts/drmaa_external_killer.py #external_chown_script = /share/apps/galaxy/scripts/external_chown_script.py Thank you very much, Richard On Oct 7, 2015, at 8:40 AM, John Chilton mailto:jmchil...@gmail.com>> wrote: Do you have drmaa_external_** options set in config/galaxy.ini? It seems like maybe you do. I would try to get Galaxy working without those first, just submitting everything as the Galaxy user. -John On Fri, Oct 2, 2015 at 4:05 PM, Richard Polich mailto:rpol...@txbiomed.org>> wrote: Hi All, Trying to setup a Galaxy cluster using Rocks Gridengine OS is Centos 6.5. psql (9.1.18) shell bash Getting error messages in paster.log below. I can submit jobs to Gridengine using qsub so this is not an issue. But when trying to "Upload File from you computer”, history indicates jobs does not complete. Any help would be appreciated. galaxy.tools.actions.upload_common DEBUG 2015-10-02 09:35:02,272 Changing ownership of /share/apps/galaxy/database/tmp/upload_file_data_xvpaYs with: /usr/bin/sudo -E /share/apps/galaxy/scripts/external_chown_script.py /share/apps/galaxy/database/tmp/upload_file_data_xvpaYs rpolich 507 galaxy.tools.actions.upload_common WARNING 2015-10-02 09:35:02,297 Changing ownership of uploaded file /share/apps/galaxy/database/tmp/upload_file_data_xvpaYs failed: sudo: no tty present and no askpass program specified galaxy.tools.actions.upload_common DEBUG 2015-10-02 09:35:02,297 Changing ownership of /share/apps/galaxy/database/tmp/tmplIgC3n with: /usr/bin/sudo -E /share/apps/galaxy/scripts/external_chown_script.py /share/apps/galaxy/database/tmp/tmplIgC3n rpolich 507 galaxy.tools.actions.upload_common WARNING 2015-10-02 09:35:02,323 Changing ownership of uploaded file /share/apps/galaxy/database/tmp/tmplIgC3n failed: sudo: no tty present and no askpass program specified galaxy.tools.actions.upload_common INFO 2015-10-02 09:35:02,357 tool upload1 created job id 101 galaxy.tools.execute DEBUG 2015-10-02 09:35:02,423 Tool [upload1] created job [101] (332.351 ms) 206.124.61.6 - - [02/Oct/2015:09:34:59 -0500] "POST /api/tools HTTP/1.1" 200 - "http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0" 206.124.61.6 - - [02/Oct/2015:09:35:02 -0500] "GET /api/histories/1fad1eaf5f4f1766/contents HTTP/1.1" 200 - "http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0" galaxy.jobs DEBUG 2015-10-02 09:35:02,676 (101) Working directory for job is: /share/apps/galaxy/database/job_working_directory/000/101 galaxy.jobs.handler DEBUG 2015-10-02 09:35:02,682 (101) Dispatching to drmaa runner galaxy.jobs DEBUG 2015-10-02 09:35:02,894 (101) Persisting job destination (destination id: sge_default) galaxy.jobs.runners DEBUG 2015-10-02 09:35:02,903 Job [101] queued (220.456 ms) galaxy.jobs.handler INFO 2015-10-02 09:35:02,958 (101) Job dispatched galaxy.jobs.command_factory INFO 2015-10-02 09:35:03,821 Built script [/share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh] for tool command[/share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh] galaxy.jobs.runners DEBUG 2015-10-02 09:35:04,010 (101) command is: /share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh; return_code=$?; python "/share/apps/galaxy/database/job_working_directory/000/101/set_metadata_QaaegG.py" "/share/apps/galaxy/database/tmp/tmpglze54" "/share/apps/galaxy/database/job_working_directory/000/101/galaxy.json" "/share/apps/galaxy/database/job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_71_7DAllZ,/share/apps/galaxy/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetAssociation_71_YiPkTL,/share/apps/galaxy/database/job_working_directory/000/101/metadata_out_HistoryDatasetAssociation_71_JbkolS,/share/apps/galaxy/database/job_working_directory/000/101/metadata_results_HistoryDatasetAssociation_71_d93tKG,/share/apps/galaxy/database/job_working_directory/000/101/galaxy_dataset_71.dat,/share/apps/galaxy/database/job_working_directory/000/101/metadata_override_HistoryDatasetAssociation_71_ih81Fj" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,074 (101) submitting file /share/apps/galaxy/database/job_working_directory/000/101/galaxy_101.sh galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,075 (101) native specification is: -q galaxy.q -V galaxy.jobs DEBUG 2015-10-02 09:35:04,075 (101) Changing ownership of working directory with: /usr/bin/sudo -E /share/apps/galaxy/scripts/external_chown_script.py /share/apps/galaxy/database/job_workin
Re: [galaxy-dev] Problems with Galaxy cluster using grid engine
Do you have drmaa_external_** options set in config/galaxy.ini? It seems like maybe you do. I would try to get Galaxy working without those first, just submitting everything as the Galaxy user. -John On Fri, Oct 2, 2015 at 4:05 PM, Richard Polich wrote: > Hi All, > > Trying to setup a Galaxy cluster using Rocks Gridengine > > OS is Centos 6.5. > psql (9.1.18) > shell bash > > Getting error messages in paster.log below. I can submit jobs to Gridengine > using qsub so this is not an issue. But when trying to "Upload File from you > computer”, history indicates jobs does not complete. > > Any help would be appreciated. > > galaxy.tools.actions.upload_common DEBUG 2015-10-02 09:35:02,272 Changing > ownership of /share/apps/galaxy/database/tmp/upload_file_data_xvpaYs with: > /usr/bin/sudo -E /share/apps/galaxy/scripts/external_chown_script.py > /share/apps/galaxy/database/tmp/upload_file_data_xvpaYs rpolich 507 > galaxy.tools.actions.upload_common WARNING 2015-10-02 09:35:02,297 Changing > ownership of uploaded file > /share/apps/galaxy/database/tmp/upload_file_data_xvpaYs failed: sudo: no tty > present and no askpass program specified > > galaxy.tools.actions.upload_common DEBUG 2015-10-02 09:35:02,297 Changing > ownership of /share/apps/galaxy/database/tmp/tmplIgC3n with: /usr/bin/sudo > -E /share/apps/galaxy/scripts/external_chown_script.py > /share/apps/galaxy/database/tmp/tmplIgC3n rpolich 507 > galaxy.tools.actions.upload_common WARNING 2015-10-02 09:35:02,323 Changing > ownership of uploaded file /share/apps/galaxy/database/tmp/tmplIgC3n failed: > sudo: no tty present and no askpass program specified > > galaxy.tools.actions.upload_common INFO 2015-10-02 09:35:02,357 tool upload1 > created job id 101 > galaxy.tools.execute DEBUG 2015-10-02 09:35:02,423 Tool [upload1] created > job [101] (332.351 ms) > 206.124.61.6 - - [02/Oct/2015:09:34:59 -0500] "POST /api/tools HTTP/1.1" 200 > - "http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel > Mac OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0" > 206.124.61.6 - - [02/Oct/2015:09:35:02 -0500] "GET > /api/histories/1fad1eaf5f4f1766/contents HTTP/1.1" 200 - > "http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel > Mac OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0" > galaxy.jobs DEBUG 2015-10-02 09:35:02,676 (101) Working directory for job > is: /share/apps/galaxy/database/job_working_directory/000/101 > galaxy.jobs.handler DEBUG 2015-10-02 09:35:02,682 (101) Dispatching to drmaa > runner > galaxy.jobs DEBUG 2015-10-02 09:35:02,894 (101) Persisting job destination > (destination id: sge_default) > galaxy.jobs.runners DEBUG 2015-10-02 09:35:02,903 Job [101] queued (220.456 > ms) > galaxy.jobs.handler INFO 2015-10-02 09:35:02,958 (101) Job dispatched > galaxy.jobs.command_factory INFO 2015-10-02 09:35:03,821 Built script > [/share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh] > for tool > command[/share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh] > galaxy.jobs.runners DEBUG 2015-10-02 09:35:04,010 (101) command is: > /share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh; > return_code=$?; python > "/share/apps/galaxy/database/job_working_directory/000/101/set_metadata_QaaegG.py" > "/share/apps/galaxy/database/tmp/tmpglze54" > "/share/apps/galaxy/database/job_working_directory/000/101/galaxy.json" > "/share/apps/galaxy/database/job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_71_7DAllZ,/share/apps/galaxy/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetAssociation_71_YiPkTL,/share/apps/galaxy/database/job_working_directory/000/101/metadata_out_HistoryDatasetAssociation_71_JbkolS,/share/apps/galaxy/database/job_working_directory/000/101/metadata_results_HistoryDatasetAssociation_71_d93tKG,/share/apps/galaxy/database/job_working_directory/000/101/galaxy_dataset_71.dat,/share/apps/galaxy/database/job_working_directory/000/101/metadata_override_HistoryDatasetAssociation_71_ih81Fj" > 5242880; sh -c "exit $return_code" > galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,074 (101) submitting > file /share/apps/galaxy/database/job_working_directory/000/101/galaxy_101.sh > galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,075 (101) native > specification is: -q galaxy.q -V > galaxy.jobs DEBUG 2015-10-02 09:35:04,075 (101) Changing ownership of > working directory with: /usr/bin/sudo -E > /share/apps/galaxy/scripts/external_chown_script.py > /share/apps/galaxy/database/job_working_directory/000/101 rpolich 507 > galaxy.jobs ERROR 2015-10-02 09:35:04,102 (101) Failed to change ownership > of /share/apps/galaxy/database/job_working_directory/000/101, making > world-writable instead > Traceback (most recent call last): > File "/share/apps/galaxy/lib/galaxy/jobs/__init__.py", line 1649, in > change_ownership_for_run > self._change_ownership( self.user_system_pwent[0], str( > self.user_system_pwent[3] ) ) > File "/share/apps/g
[galaxy-dev] Problems with Galaxy cluster using grid engine
Hi All, Trying to setup a Galaxy cluster using Rocks Gridengine OS is Centos 6.5. psql (9.1.18) shell bash Getting error messages in paster.log below. I can submit jobs to Gridengine using qsub so this is not an issue. But when trying to "Upload File from you computer”, history indicates jobs does not complete. Any help would be appreciated. galaxy.tools.actions.upload_common DEBUG 2015-10-02 09:35:02,272 Changing ownership of /share/apps/galaxy/database/tmp/upload_file_data_xvpaYs with: /usr/bin/sudo -E /share/apps/galaxy/scripts/external_chown_script.py /share/apps/galaxy/database/tmp/upload_file_data_xvpaYs rpolich 507 galaxy.tools.actions.upload_common WARNING 2015-10-02 09:35:02,297 Changing ownership of uploaded file /share/apps/galaxy/database/tmp/upload_file_data_xvpaYs failed: sudo: no tty present and no askpass program specified galaxy.tools.actions.upload_common DEBUG 2015-10-02 09:35:02,297 Changing ownership of /share/apps/galaxy/database/tmp/tmplIgC3n with: /usr/bin/sudo -E /share/apps/galaxy/scripts/external_chown_script.py /share/apps/galaxy/database/tmp/tmplIgC3n rpolich 507 galaxy.tools.actions.upload_common WARNING 2015-10-02 09:35:02,323 Changing ownership of uploaded file /share/apps/galaxy/database/tmp/tmplIgC3n failed: sudo: no tty present and no askpass program specified galaxy.tools.actions.upload_common INFO 2015-10-02 09:35:02,357 tool upload1 created job id 101 galaxy.tools.execute DEBUG 2015-10-02 09:35:02,423 Tool [upload1] created job [101] (332.351 ms) 206.124.61.6 - - [02/Oct/2015:09:34:59 -0500] "POST /api/tools HTTP/1.1" 200 - "http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0" 206.124.61.6 - - [02/Oct/2015:09:35:02 -0500] "GET /api/histories/1fad1eaf5f4f1766/contents HTTP/1.1" 200 - "http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0" galaxy.jobs DEBUG 2015-10-02 09:35:02,676 (101) Working directory for job is: /share/apps/galaxy/database/job_working_directory/000/101 galaxy.jobs.handler DEBUG 2015-10-02 09:35:02,682 (101) Dispatching to drmaa runner galaxy.jobs DEBUG 2015-10-02 09:35:02,894 (101) Persisting job destination (destination id: sge_default) galaxy.jobs.runners DEBUG 2015-10-02 09:35:02,903 Job [101] queued (220.456 ms) galaxy.jobs.handler INFO 2015-10-02 09:35:02,958 (101) Job dispatched galaxy.jobs.command_factory INFO 2015-10-02 09:35:03,821 Built script [/share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh] for tool command[/share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh] galaxy.jobs.runners DEBUG 2015-10-02 09:35:04,010 (101) command is: /share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh; return_code=$?; python "/share/apps/galaxy/database/job_working_directory/000/101/set_metadata_QaaegG.py" "/share/apps/galaxy/database/tmp/tmpglze54" "/share/apps/galaxy/database/job_working_directory/000/101/galaxy.json" "/share/apps/galaxy/database/job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_71_7DAllZ,/share/apps/galaxy/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetAssociation_71_YiPkTL,/share/apps/galaxy/database/job_working_directory/000/101/metadata_out_HistoryDatasetAssociation_71_JbkolS,/share/apps/galaxy/database/job_working_directory/000/101/metadata_results_HistoryDatasetAssociation_71_d93tKG,/share/apps/galaxy/database/job_working_directory/000/101/galaxy_dataset_71.dat,/share/apps/galaxy/database/job_working_directory/000/101/metadata_override_HistoryDatasetAssociation_71_ih81Fj" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,074 (101) submitting file /share/apps/galaxy/database/job_working_directory/000/101/galaxy_101.sh galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,075 (101) native specification is: -q galaxy.q -V galaxy.jobs DEBUG 2015-10-02 09:35:04,075 (101) Changing ownership of working directory with: /usr/bin/sudo -E /share/apps/galaxy/scripts/external_chown_script.py /share/apps/galaxy/database/job_working_directory/000/101 rpolich 507 galaxy.jobs ERROR 2015-10-02 09:35:04,102 (101) Failed to change ownership of /share/apps/galaxy/database/job_working_directory/000/101, making world-writable instead Traceback (most recent call last): File "/share/apps/galaxy/lib/galaxy/jobs/__init__.py", line 1649, in change_ownership_for_run self._change_ownership( self.user_system_pwent[0], str( self.user_system_pwent[3] ) ) File "/share/apps/galaxy/lib/galaxy/jobs/__init__.py", line 1643, in _change_ownership assert p.returncode == 0 AssertionError galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,102 (101) submitting with credentials: rpolich [uid: 1006] galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,104 (101) Job script for external submission is: /share/apps/galaxy/database/gridengine/10
