June 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 2fc266: fixed $defaults according to #2430
by GitHub 03 Jun '16

03 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2fc266e4ab8b0cd0a1c6a0ecbd0cb9615f8a4eb2 https://github.com/galaxyproject/galaxy/commit/2fc266e4ab8b0cd0a1c6a0ecbd0c… Author: Thomas Wollmann <thomas.wollmann(a)bioquant.uni-heidelberg.de> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- fixed $defaults according to #2430 Commit: 1695994c84caeb07770f33e41f9408eaa30e24dd https://github.com/galaxyproject/galaxy/commit/1695994c84caeb07770f33e41f94… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- polish Commit: 697b01c211f0efbd0be5cc45c860e0c6f6e72ad6 https://github.com/galaxyproject/galaxy/commit/697b01c211f0efbd0be5cc45c860… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2438 from ThomasWollmann/dev fixed $defaults according to #2430 Compare: https://github.com/galaxyproject/galaxy/compare/a0dbcb93a3cb...697b01c211f0

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[galaxyproject/galaxy] 52a5f6: Properly display subworkflows in new run workflow ...
by GitHub 02 Jun '16

02 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 52a5f6e2dbf24202258973c706e08f15d1d5a44b https://github.com/galaxyproject/galaxy/commit/52a5f6e2dbf24202258973c706e0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Properly display subworkflows in new run workflow form Commit: dcd07221a8a00250dc8dc171ab480d8ba7f3b323 https://github.com/galaxyproject/galaxy/commit/dcd07221a8a00250dc8dc171ab48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Remove output details from success message Commit: 7eaf40ec56ed186289972883410b059ded993e7b https://github.com/galaxyproject/galaxy/commit/7eaf40ec56ed186289972883410b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Re-add new history links to success message Commit: 1b3eaeb299bb29460c1ebd24c881d2921631987b https://github.com/galaxyproject/galaxy/commit/1b3eaeb299bb29460c1ebd24c881… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Fix batchmode labels Commit: a0dbcb93a3cb1e3a108b07272946e9fe36e0b376 https://github.com/galaxyproject/galaxy/commit/a0dbcb93a3cb1e3a108b07272946… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-select-content.js M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2440 from guerler/fix_subworkflows_display Properly list subworkflows in run workflow form Compare: https://github.com/galaxyproject/galaxy/compare/84ece6da372e...a0dbcb93a3cb

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[galaxyproject/galaxy] a27e86: wrap bare str raises with generic Exception()
by GitHub 02 Jun '16

02 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a27e86786ad031eafcbfeb39ffdadf71d80dcfad https://github.com/galaxyproject/galaxy/commit/a27e86786ad031eafcbfeb39ffda… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/repository_types/metadata.py M tools/filters/axt_to_lav.py Log Message: ----------- wrap bare str raises with generic Exception() as Pyton 2.7 does not support bare str Commit: fe64a8198bca75f2e535efc7c3813d24810904ab https://github.com/galaxyproject/galaxy/commit/fe64a8198bca75f2e535efc7c381… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- fix the mess made with mass edit Commit: 6094990e43f6510833395885d234a2264e7d44f1 https://github.com/galaxyproject/galaxy/commit/6094990e43f6510833395885d234… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/repository_types/metadata.py M tools/filters/axt_to_lav.py Log Message: ----------- Merge pull request #2424 from martenson/port-exceptionwrap-16.04 [16.04] wrap bare str exceptions Commit: 214e757d81623e9c12d171f3dcfc516c7dcc5e32 https://github.com/galaxyproject/galaxy/commit/214e757d81623e9c12d171f3dcfc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Only scan the last 16 MB of a job's stderr for slurm memory warning messages. Commit: dcb28e095012fef3be769f677fa572f13d4ed88a https://github.com/galaxyproject/galaxy/commit/dcb28e095012fef3be769f677fa5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix linting error Commit: ceb825bea8b28c8908c8a719919b9167bedabe55 https://github.com/galaxyproject/galaxy/commit/ceb825bea8b28c8908c8a719919b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2432 from natefoo/job-output-memory-fix [16.04] Only scan the last 16 MB of a job's stderr for slurm memory warning messages Commit: 7cb527ac595591c99401436757168b366f86a526 https://github.com/galaxyproject/galaxy/commit/7cb527ac595591c9940143675716… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Overwrite the correct part of stderr - Skip partial line - Seek back to the correct position after readlines() - Use the same approach in __check_memory_limit() Commit: 58f3f5c7dd4c622adce0f18d24a0ee950d1d4dfd https://github.com/galaxyproject/galaxy/commit/58f3f5c7dd4c622adce0f18d24a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2447 from nsoranzo/release_16.04_fix_for_2432 [16.04] Overwrite the correct part of stderr Commit: 84ece6da372ea0e0537bf68c6981962437e0d330 https://github.com/galaxyproject/galaxy/commit/84ece6da372ea0e0537bf68c6981… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ec476c7cb46a...84ece6da372e

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[galaxyproject/galaxy] 7cb527: Overwrite the correct part of stderr
by GitHub 02 Jun '16

02 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 7cb527ac595591c99401436757168b366f86a526 https://github.com/galaxyproject/galaxy/commit/7cb527ac595591c9940143675716… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Overwrite the correct part of stderr - Skip partial line - Seek back to the correct position after readlines() - Use the same approach in __check_memory_limit() Commit: 58f3f5c7dd4c622adce0f18d24a0ee950d1d4dfd https://github.com/galaxyproject/galaxy/commit/58f3f5c7dd4c622adce0f18d24a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2447 from nsoranzo/release_16.04_fix_for_2432 [16.04] Overwrite the correct part of stderr Compare: https://github.com/galaxyproject/galaxy/compare/ceb825bea8b2...58f3f5c7dd4c

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[galaxyproject/infrastructure-playbook] fd36ee: Allow Galaxy Team members to log in to cvmfs0-tacc...
by GitHub 02 Jun '16

02 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fd36eee5572fe6871216411fe85dc892ae8e3b6e https://github.com/galaxyproject/infrastructure-playbook/commit/fd36eee5572… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M galaxyenv/host_vars/cvmfs0-tacc0.galaxyproject.org.yml M roles/cvmfs/defaults/main.yml M roles/cvmfs/tasks/stratum0.yml M roles/cvmfs/tasks/stratum1.yml A taccenv/host_vars/galaxy04.tacc.utexas.edu.yml M taccenv/inventory M taccenv/playbook.yml A taccenv/secret_group_vars/baseenv.yml A taccenv/secret_group_vars/galaxymainservers.yml A taccenv/secret_group_vars/galaxytestservers.yml A taccenv/secret_host_vars/default.yml A taccenv/secret_host_vars/galaxy04.tacc.utexas.edu.yml Log Message: ----------- Allow Galaxy Team members to log in to cvmfs0-tacc0 to update Test and Main. Stratum1 and client permissions coming soon.

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[galaxyproject/galaxy] d45890: Raven: fix import in galaxy.panels.mako
by GitHub 02 Jun '16

02 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d458906f37239be23552cf9df86dfa066270e54c https://github.com/galaxyproject/galaxy/commit/d458906f37239be23552cf9df86d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Raven: fix import in galaxy.panels.mako Raven now uses a UMD and checks for requirejs removing it from globals if found. This adds a require import to load Raven. Commit: 8ef5279aacc6125908a37a9157feb47c7c556104 https://github.com/galaxyproject/galaxy/commit/8ef5279aacc6125908a37a9157fe… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Raven: revert previous commit and move raven first Moves galaxy.panels.mako's import of Raven back to vanilla script tag and before the requirejs library import, allowing Raven's UMD to define Raven as a global. This starts Raven/sentry *before* the library package is loaded so that library errors can be captured as well. Commit: f78d5404a27d13e0a4e14e655673357d1497f7b2 https://github.com/galaxyproject/galaxy/commit/f78d5404a27d13e0a4e14e655673… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M client/bower.json R client/galaxy/scripts/libs/tracekit.js M client/grunt-tasks/install-libs.js R static/maps/libs/tracekit.js.map R static/scripts/libs/tracekit.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako Log Message: ----------- Raven: remove tracekit as raven has its own Commit: ec476c7cb46a89ae222a65ff8fe0bb468d989bfd https://github.com/galaxyproject/galaxy/commit/ec476c7cb46a89ae222a65ff8fe0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M client/bower.json R client/galaxy/scripts/libs/tracekit.js M client/grunt-tasks/install-libs.js R static/maps/libs/tracekit.js.map R static/scripts/libs/tracekit.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #2445 from carlfeberhard/fix.raven Fix raven.js import order in galaxy.panels.mako Compare: https://github.com/galaxyproject/galaxy/compare/25a26d8c9c4f...ec476c7cb46a

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[galaxyproject/usegalaxy-playbook] 9d2ecd: Update Main version number
by GitHub 01 Jun '16

01 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9d2ecd436ca214a4310df316324923f3108300fd https://github.com/galaxyproject/usegalaxy-playbook/commit/9d2ecd436ca214a4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main version number

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[galaxyproject/infrastructure-playbook] 341a94: Terminate some TACC Jetstream instances
by GitHub 01 Jun '16

01 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 341a94ce6a547a2e6c360cf0079a90caa0e80bb7 https://github.com/galaxyproject/infrastructure-playbook/commit/341a94ce6a5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- Terminate some TACC Jetstream instances

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[galaxyproject/infrastructure-playbook] 302dff: Jetstream controllers are in DNS
by GitHub 01 Jun '16

01 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 302dff7c2bb118e6a081464939d1eb8dde596b10 https://github.com/galaxyproject/infrastructure-playbook/commit/302dff7c2bb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: M jetstreamiuenv/inventory M jetstreamtaccenv/inventory Log Message: ----------- Jetstream controllers are in DNS

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[galaxyproject/usegalaxy-playbook] d50bdf: Enable stats for main, segment test/main.
by GitHub 01 Jun '16

01 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d50bdf0ccf5debd83dccd87bc1cbbd40cf7f153e https://github.com/galaxyproject/usegalaxy-playbook/commit/d50bdf0ccf5debd8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Enable stats for main, segment test/main.

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