galaxy-commits April 2016

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[galaxyproject/galaxy] 84ad9c: Rev Pulsar to 0.7.0.dev3.
by GitHub 12 Apr '16

12 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84ad9c2ee2c5cf0420f837405dfbd1893f1d0ed2 https://github.com/galaxyproject/galaxy/commit/84ad9c2ee2c5cf0420f837405dfb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-10 (Sun, 10 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Rev Pulsar to 0.7.0.dev3. - Fixes numerous problems mostly notably fixes external metadata generation and job metrics collection for recent Pulsar. This was broken when tools were given clean working directory. - Produce a new message if an older Pulsar version is targetted via REST of library (should help with upgrading to Galaxy 16.04). - Newer pulsar lib allows more flexible configuration of managers - update documntation to reflect this. Commit: 27f418c52d685d41646fa6cf932e8144fef63bb5 https://github.com/galaxyproject/galaxy/commit/27f418c52d685d41646fa6cf932e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R install_and_test_tool_shed_repositories.sh R scripts/tool_shed/check_repositories_for_functional_tests.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py Log Message: ----------- Remove scripts which depend on install_and_test_tool_shed_repositories. Commit: a9d675f5e854de8634789fca54bb88c6a9f5de2c https://github.com/galaxyproject/galaxy/commit/a9d675f5e854de8634789fca54bb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Fix sys.path.insert() after #2093. Commit: ceeb01d84e7f510fab39626dec7f7d537a66f2fd https://github.com/galaxyproject/galaxy/commit/ceeb01d84e7f510fab39626dec7f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R install_and_test_tool_shed_repositories.sh M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_repositories_for_functional_tests.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Merge pull request #2133 from nsoranzo/release_16.04_fix_for_2093 [16.04] Fixes due to #2093 and #2018 Commit: f03c0375566a835b9e75135ba9462ddad1dfeb70 https://github.com/galaxyproject/galaxy/commit/f03c0375566a835b9e75135ba946… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #2122 from jmchilton/pulsar_metadata [16.04] Rev Pulsar to 0.7.0.dev3. Commit: 408827e251f92cdc5b6c794272a6ba2dc1473780 https://github.com/galaxyproject/galaxy/commit/408827e251f92cdc5b6c794272a6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced R install_and_test_tool_shed_repositories.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_repositories_for_functional_tests.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/baf1bd639f17...408827e251f9

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[galaxyproject/galaxy] 84ad9c: Rev Pulsar to 0.7.0.dev3.
by GitHub 12 Apr '16

12 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 84ad9c2ee2c5cf0420f837405dfbd1893f1d0ed2 https://github.com/galaxyproject/galaxy/commit/84ad9c2ee2c5cf0420f837405dfb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-10 (Sun, 10 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Rev Pulsar to 0.7.0.dev3. - Fixes numerous problems mostly notably fixes external metadata generation and job metrics collection for recent Pulsar. This was broken when tools were given clean working directory. - Produce a new message if an older Pulsar version is targetted via REST of library (should help with upgrading to Galaxy 16.04). - Newer pulsar lib allows more flexible configuration of managers - update documntation to reflect this. Commit: f03c0375566a835b9e75135ba9462ddad1dfeb70 https://github.com/galaxyproject/galaxy/commit/f03c0375566a835b9e75135ba946… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #2122 from jmchilton/pulsar_metadata [16.04] Rev Pulsar to 0.7.0.dev3. Compare: https://github.com/galaxyproject/galaxy/compare/ceeb01d84e7f...f03c0375566a

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[galaxyproject/galaxy] 27f418: Remove scripts which depend on install_and_test_to...
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 27f418c52d685d41646fa6cf932e8144fef63bb5 https://github.com/galaxyproject/galaxy/commit/27f418c52d685d41646fa6cf932e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R install_and_test_tool_shed_repositories.sh R scripts/tool_shed/check_repositories_for_functional_tests.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py Log Message: ----------- Remove scripts which depend on install_and_test_tool_shed_repositories. Commit: a9d675f5e854de8634789fca54bb88c6a9f5de2c https://github.com/galaxyproject/galaxy/commit/a9d675f5e854de8634789fca54bb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Fix sys.path.insert() after #2093. Commit: ceeb01d84e7f510fab39626dec7f7d537a66f2fd https://github.com/galaxyproject/galaxy/commit/ceeb01d84e7f510fab39626dec7f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R install_and_test_tool_shed_repositories.sh M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_repositories_for_functional_tests.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Merge pull request #2133 from nsoranzo/release_16.04_fix_for_2093 [16.04] Fixes due to #2093 and #2018 Compare: https://github.com/galaxyproject/galaxy/compare/6317297cad4e...ceeb01d84e7f

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[galaxyproject/galaxy] abca52: Merge pull request #2118 from jmchilton/version-16...
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: abca525bee723fab9027c7fb5554a16b319976ab https://github.com/galaxyproject/galaxy/commit/abca525bee723fab9027c7fb5554… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #2118 from jmchilton/version-16.04 [16.04] Update version to 16.04.rc1 Commit: f759961a29eeb28c6140d5d206bfd93fbdbfd379 https://github.com/galaxyproject/galaxy/commit/f759961a29eeb28c6140d5d206bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- mention planemo in the error message for disabled TS pushing rephrase to Norwegian Commit: fe4afefc42a45faca09c7c2aea34a97cad02be76 https://github.com/galaxyproject/galaxy/commit/fe4afefc42a45faca09c7c2aea34… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #2114 from martenson/planemo-mention [16.01] mention planemo in the error message for disabled TS pushing Commit: f2bd242a2c28954215fb84d289d19e35a6460c65 https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d1… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- change run_tool_shed.py to see the file in the correct lcoation Commit: 5f01cddc4b2a1e0578a2d6dde73b05fe6d95a0a7 https://github.com/galaxyproject/galaxy/commit/5f01cddc4b2a1e0578a2d6dde73b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #2131 from nturaga/16.04_toolshed_fix [16.04] change run_tool_shed.py to see the file in the correct lcoation Commit: 6317297cad4e51f25c58a375dedd5d1e3f1f650a https://github.com/galaxyproject/galaxy/commit/6317297cad4e51f25c58a375dedd… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: baf1bd639f175c6f06fd840a57ec44c8e612841a https://github.com/galaxyproject/galaxy/commit/baf1bd639f175c6f06fd840a57ec… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/03b9f7c372f2...baf1bd639f17

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[galaxyproject/galaxy] f75996: mention planemo in the error message for disabled ...
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: f759961a29eeb28c6140d5d206bfd93fbdbfd379 https://github.com/galaxyproject/galaxy/commit/f759961a29eeb28c6140d5d206bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- mention planemo in the error message for disabled TS pushing rephrase to Norwegian Commit: fe4afefc42a45faca09c7c2aea34a97cad02be76 https://github.com/galaxyproject/galaxy/commit/fe4afefc42a45faca09c7c2aea34… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #2114 from martenson/planemo-mention [16.01] mention planemo in the error message for disabled TS pushing Commit: 6317297cad4e51f25c58a375dedd5d1e3f1f650a https://github.com/galaxyproject/galaxy/commit/6317297cad4e51f25c58a375dedd… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/5f01cddc4b2a...6317297cad4e

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[galaxyproject/galaxy] f2bd24: change run_tool_shed.py to see the file in the cor...
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: f2bd242a2c28954215fb84d289d19e35a6460c65 https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d1… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- change run_tool_shed.py to see the file in the correct lcoation Commit: 5f01cddc4b2a1e0578a2d6dde73b05fe6d95a0a7 https://github.com/galaxyproject/galaxy/commit/5f01cddc4b2a1e0578a2d6dde73b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #2131 from nturaga/16.04_toolshed_fix [16.04] change run_tool_shed.py to see the file in the correct lcoation Compare: https://github.com/galaxyproject/galaxy/compare/abca525bee72...5f01cddc4b2a

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[galaxyproject/infrastructure-playbook] 8b299c: Install git on controllers
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8b299c5d265ef1ce20e3373e683505e80eaf3eaf https://github.com/galaxyproject/infrastructure-playbook/commit/8b299c5d265… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/controllers.yml Log Message: ----------- Install git on controllers

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[galaxyproject/infrastructure-playbook] 11a4c7: Jetstream NFS and CVMFS updates for Main
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 11a4c763507995bba69c47a38d9db4da78fbc868 https://github.com/galaxyproject/infrastructure-playbook/commit/11a4c763507… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamiuenv/inventory M jetstreamtaccenv/group_vars/galaxynodes.yml M jetstreamtaccenv/inventory M roles/cvmfs/defaults/main.yml M roles/jetstream_nfs/tasks/main.yml M taccenv/group_vars/galaxyservers.yml M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Jetstream NFS and CVMFS updates for Main

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[galaxyproject/infrastructure-playbook] 10e2dd: Export Jetstream NFS to all TACC galaxy VMs
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 10e2dd1f4c1a5890cdcf8cb3511fcc402590af15 https://github.com/galaxyproject/infrastructure-playbook/commit/10e2dd1f4c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M roles/jetstream_nfs/tasks/server.yml Log Message: ----------- Export Jetstream NFS to all TACC galaxy VMs

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[galaxyproject/galaxy] f75996: mention planemo in the error message for disabled ...
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f759961a29eeb28c6140d5d206bfd93fbdbfd379 https://github.com/galaxyproject/galaxy/commit/f759961a29eeb28c6140d5d206bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- mention planemo in the error message for disabled TS pushing rephrase to Norwegian Commit: fe4afefc42a45faca09c7c2aea34a97cad02be76 https://github.com/galaxyproject/galaxy/commit/fe4afefc42a45faca09c7c2aea34… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #2114 from martenson/planemo-mention [16.01] mention planemo in the error message for disabled TS pushing Compare: https://github.com/galaxyproject/galaxy/compare/455113d18223...fe4afefc42a4

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galaxy-commits April 2016