July 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 66dabf: Add ptkscmp datatype for PlantTribes significant c...
by GitHub 04 Jul '17

04 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 66dabf65ab3d3e9e2d59fefb57526b931a5920fe https://github.com/galaxyproject/galaxy/commit/66dabf65ab3d3e9e2d59fefb5752… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/plant_tribes.py A lib/galaxy/datatypes/test/1.ptkscmp Log Message: ----------- Add ptkscmp datatype for PlantTribes significant components in the Ks distribution Commit: ac59d1d6e042dd3288e89de48c470751db75de48 https://github.com/galaxyproject/galaxy/commit/ac59d1d6e042dd3288e89de48c47… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-04 (Tue, 04 Jul 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/plant_tribes.py A lib/galaxy/datatypes/test/1.ptkscmp Log Message: ----------- Merge pull request #4259 from gregvonkuster/ptkscmp Add ptkscmp datatype Compare: https://github.com/galaxyproject/galaxy/compare/666c4bcbb010...ac59d1d6e042

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[galaxyproject/galaxy] f8c2c0: Add shared history grid to client
by GitHub 03 Jul '17

03 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8c2c0b0355b69f279c1e05fc0b3a5caba1bdb77 https://github.com/galaxyproject/galaxy/commit/f8c2c0b0355b69f279c1e05fc0b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-29 (Thu, 29 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/options-menu.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/history/options-menu.js Log Message: ----------- Add shared history grid to client Commit: 5de92dfbf4637b65930c2d6782db5ca7b9735646 https://github.com/galaxyproject/galaxy/commit/5de92dfbf4637b65930c2d6782db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-29 (Thu, 29 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/options-menu.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/history/history-list.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- Restore basic copy and unshare operations Commit: fb73b5dc14e680b9488d0c82b44091adee94df8e https://github.com/galaxyproject/galaxy/commit/fb73b5dc14e680b9488d0c82b440… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-29 (Thu, 29 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Align operation handling Commit: d694b6061326d8747f3fa282c5bdf8257261252e https://github.com/galaxyproject/galaxy/commit/d694b6061326d8747f3fa282c5bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-29 (Thu, 29 Jun 2017) Changed paths: R templates/webapps/galaxy/history/shared_grid.mako Log Message: ----------- Remove shared grids mako Commit: 666c4bcbb010c348d1ad4e940475ebc46f610a89 https://github.com/galaxyproject/galaxy/commit/666c4bcbb010c348d1ad4e940475… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-03 (Mon, 03 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/options-menu.js R templates/webapps/galaxy/history/shared_grid.mako Log Message: ----------- Merge remote-tracking branch 'guerler/fix_shared_history' into dev Compare: https://github.com/galaxyproject/galaxy/compare/bc8d6dd1da33...666c4bcbb010

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[galaxyproject/galaxy] 36bdd9: Keep tool parameters when rerunning a job
by GitHub 03 Jul '17

03 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 36bdd99fbc2875425f0c0e9861f4238f968baecb https://github.com/galaxyproject/galaxy/commit/36bdd99fbc2875425f0c0e9861f4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-30 (Fri, 30 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/jobs.py M static/maps/mvc/tool/tool-form-base.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-base.js Log Message: ----------- Keep tool parameters when rerunning a job with a different tool version, as long as the parameter did not change. Addresses https://github.com/galaxyproject/galaxy/issues/1729 Commit: 65e3365948ae84da2f1ccaeed4030ec8fd7d7f79 https://github.com/galaxyproject/galaxy/commit/65e3365948ae84da2f1ccaeed403… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-02 (Sun, 02 Jul 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Simplify if/elif (thx @nsoranzo) Commit: 4c68e29a81fb991e3eda7efa035d0b7856a62372 https://github.com/galaxyproject/galaxy/commit/4c68e29a81fb991e3eda7efa035d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-02 (Sun, 02 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Use if/else if to determine the job_id Commit: b928236cfaf197629530277154995b1fbb75c066 https://github.com/galaxyproject/galaxy/commit/b928236cfaf19762953027715499… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-02 (Sun, 02 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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-base.js Log Message: ----------- Fix indentation Commit: bc8d6dd1da3347a2eacdcdbed081d85f16b9880c https://github.com/galaxyproject/galaxy/commit/bc8d6dd1da3347a2eacdcdbed081… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-03 (Mon, 03 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/jobs.py M static/maps/mvc/tool/tool-form-base.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-base.js Log Message: ----------- Merge pull request #4271 from mvdbeek/job_rerun_changed_parameters Keep tool parameters when rerunning a job Compare: https://github.com/galaxyproject/galaxy/compare/ee62fa7de89d...bc8d6dd1da33

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[galaxyproject/galaxy] cbcee5: Use contextmanager when using compression_util.get...
by GitHub 03 Jul '17

03 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cbcee585b5cde16ef356a0907d52a493fd1b9f53 https://github.com/galaxyproject/galaxy/commit/cbcee585b5cde16ef356a0907d52… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-30 (Fri, 30 Jun 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Use contextmanager when using compression_util.get_fileobj() Commit: e379f44effa9a72e5da6d01db6e2ee6d7f56e949 https://github.com/galaxyproject/galaxy/commit/e379f44effa9a72e5da6d01db6e2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-03 (Mon, 03 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Remove outer try/except in Eland sniffer Exceptions in a sniffer are already caught in galaxy.datatypes.sniff.guess_ext() and are equivalent to `return False`. Thanks @nsoranzo! Commit: 3d16aa62fa8e5dc2d47e92e0a8eaa1ece27fb7ee https://github.com/galaxyproject/galaxy/commit/3d16aa62fa8e5dc2d47e92e0a8ea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-03 (Mon, 03 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Also remove the inner try/except Commit: ee62fa7de89da4b6ecec04a43e608820ab6aa65e https://github.com/galaxyproject/galaxy/commit/ee62fa7de89da4b6ecec04a43e60… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-07-03 (Mon, 03 Jul 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #4270 from mvdbeek/context_manager_get_fileobj Use contextmanager when using compression_util.get_fileobj() Compare: https://github.com/galaxyproject/galaxy/compare/816912998115...ee62fa7de89d

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