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

[galaxyproject/galaxy] 3e0e96: add work on release notes 16.10, improve docs for ...
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 3e0e96657d765f4023bb6801ace2e96a1ffc4505 https://github.com/galaxyproject/galaxy/commit/3e0e96657d765f4023bb6801ace2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/admin/index.rst M doc/source/admin/webhooks.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- add work on release notes 16.10, improve docs for webhooks Conflicts: doc/source/releases/16.10.rst doc/source/releases/16.10_announce.rst Commit: 739fb59cba5b7747a32e685a3632f96effad4c11 https://github.com/galaxyproject/galaxy/commit/739fb59cba5b7747a32e685a3632… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- fix the fix Commit: 5784a838a554f8dcf9e132e26be01240a37a3e65 https://github.com/galaxyproject/galaxy/commit/5784a838a554f8dcf9e132e26be0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/releases/16.10.rst Log Message: ----------- fix bad merge Commit: 83de83e7edc230d7f9841a6d9770d87d0c89d06f https://github.com/galaxyproject/galaxy/commit/83de83e7edc230d7f9841a6d9770… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/admin/index.rst M doc/source/admin/webhooks.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- Merge pull request #3282 from martenson/release_16.10 [16.10] work on release notes 16.10 Compare: https://github.com/galaxyproject/galaxy/compare/d0f39ceff518...83de83e7edc2

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[galaxyproject/galaxy] a84601: Add 16.10 release notes.
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a84601ba80cb8620a396e740e9a69f3d6f1dfd37 https://github.com/galaxyproject/galaxy/commit/a84601ba80cb8620a396e740e9a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Add 16.10 release notes. Commit: 8766e125091d0a5a83a0fd4daf274fe93551a443 https://github.com/galaxyproject/galaxy/commit/8766e125091d0a5a83a0fd4daf27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.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/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Escape filename in upload dialog, default and composite. Pointed out by David Wyde. Commit: 13ab07030c8ffa5012a123671c2ab450bf14c40b https://github.com/galaxyproject/galaxy/commit/13ab07030c8ffa5012a123671c2a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use consistent spacing. Commit: 75d327f165c730f95e181a2feff1db64074ab3e6 https://github.com/galaxyproject/galaxy/commit/75d327f165c730f95e181a2feff1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.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/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #3278 from dannon/upload_escape_filename [16.10] Escape filename in upload dialog, default and composite. Commit: f6b94dc465a41e0ce25cd0d38b8cfa81ab4c5254 https://github.com/galaxyproject/galaxy/commit/f6b94dc465a41e0ce25cd0d38b8c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Fix for ToolShed install when copied sample data target exists, but is broken symlink. Commit: 70fc43b24090e537479a74b34a7ff9bc4e43de84 https://github.com/galaxyproject/galaxy/commit/70fc43b24090e537479a74b34a7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Merge pull request #3279 from blankenberg/16.10_ts_install_broken_symlink [16.10] Fix for ToolShed install when copied sample data target exists, but is broken symlink. Commit: d0f39ceff51843a95048dfdaf49035d07ce75c1d https://github.com/galaxyproject/galaxy/commit/d0f39ceff51843a95048dfdaf490… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3270 from jmchilton/16.10_release_notes_0 [16.10] Add 16.10 release notes. Commit: cbd527b9a4671c7abe9a22cf69e869b5d2de858a https://github.com/galaxyproject/galaxy/commit/cbd527b9a4671c7abe9a22cf69e8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M lib/tool_shed/util/tool_util.py M scripts/bootstrap_history.py M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.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/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/33dec01ba218...cbd527b9a467

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[galaxyproject/galaxy] a84601: Add 16.10 release notes.
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: a84601ba80cb8620a396e740e9a69f3d6f1dfd37 https://github.com/galaxyproject/galaxy/commit/a84601ba80cb8620a396e740e9a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Add 16.10 release notes. Commit: d0f39ceff51843a95048dfdaf49035d07ce75c1d https://github.com/galaxyproject/galaxy/commit/d0f39ceff51843a95048dfdaf490… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3270 from jmchilton/16.10_release_notes_0 [16.10] Add 16.10 release notes. Compare: https://github.com/galaxyproject/galaxy/compare/70fc43b24090...d0f39ceff518

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[galaxyproject/galaxy] f6b94d: Fix for ToolShed install when copied sample data t...
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: f6b94dc465a41e0ce25cd0d38b8cfa81ab4c5254 https://github.com/galaxyproject/galaxy/commit/f6b94dc465a41e0ce25cd0d38b8c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Fix for ToolShed install when copied sample data target exists, but is broken symlink. Commit: 70fc43b24090e537479a74b34a7ff9bc4e43de84 https://github.com/galaxyproject/galaxy/commit/70fc43b24090e537479a74b34a7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Merge pull request #3279 from blankenberg/16.10_ts_install_broken_symlink [16.10] Fix for ToolShed install when copied sample data target exists, but is broken symlink. Compare: https://github.com/galaxyproject/galaxy/compare/75d327f165c7...70fc43b24090

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[galaxyproject/galaxy] 8766e1: Escape filename in upload dialog, default and comp...
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 8766e125091d0a5a83a0fd4daf274fe93551a443 https://github.com/galaxyproject/galaxy/commit/8766e125091d0a5a83a0fd4daf27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.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/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Escape filename in upload dialog, default and composite. Pointed out by David Wyde. Commit: 13ab07030c8ffa5012a123671c2ab450bf14c40b https://github.com/galaxyproject/galaxy/commit/13ab07030c8ffa5012a123671c2a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use consistent spacing. Commit: 75d327f165c730f95e181a2feff1db64074ab3e6 https://github.com/galaxyproject/galaxy/commit/75d327f165c730f95e181a2feff1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.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/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #3278 from dannon/upload_escape_filename [16.10] Escape filename in upload dialog, default and composite. Compare: https://github.com/galaxyproject/galaxy/compare/8a5ff5df21ef...75d327f165c7

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[galaxyproject/usegalaxy-playbook] 0426a2: Update log archival for zerg mode
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0426a2361c865956c297f55561e9ff1c0bb9df51 https://github.com/galaxyproject/usegalaxy-playbook/commit/0426a2361c865956… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M roles/usegalaxy_privileged/templates/archive_logs.sh.j2 Log Message: ----------- Update log archival for zerg mode

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[galaxyproject/usegalaxy-playbook] 41fae2: Add env vars to Test jobs
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 41fae21828b968cf2c31aa08e2dfe877203b572f https://github.com/galaxyproject/usegalaxy-playbook/commit/41fae21828b968cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Add env vars to Test jobs

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[galaxyproject/galaxy] a1e396: Fix tour URLs in welcome
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1e3965eaf7e850486d289d1a2026877177b3c27 https://github.com/galaxyproject/galaxy/commit/a1e3965eaf7e850486d289d1a202… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- Fix tour URLs in welcome Commit: 8a5ff5df21efc6db7d2df47171f7cbad5cb1f608 https://github.com/galaxyproject/galaxy/commit/8a5ff5df21efc6db7d2df47171f7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- Merge pull request #3277 from dannon/fix_tour_welcome_1610 [16.10] port Fix tour URLs in welcome Commit: 33dec01ba2183d2f980947cc467dfab7f9bf4ddb https://github.com/galaxyproject/galaxy/commit/33dec01ba2183d2f980947cc467d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-07 (Wed, 07 Dec 2016) Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/cd1ae6b9d26a...33dec01ba218

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[galaxyproject/galaxy] a1e396: Fix tour URLs in welcome
by GitHub 06 Dec '16

06 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: a1e3965eaf7e850486d289d1a2026877177b3c27 https://github.com/galaxyproject/galaxy/commit/a1e3965eaf7e850486d289d1a202… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- Fix tour URLs in welcome Commit: 8a5ff5df21efc6db7d2df47171f7cbad5cb1f608 https://github.com/galaxyproject/galaxy/commit/8a5ff5df21efc6db7d2df47171f7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- Merge pull request #3277 from dannon/fix_tour_welcome_1610 [16.10] port Fix tour URLs in welcome Compare: https://github.com/galaxyproject/galaxy/compare/d0ad2ae1ce29...8a5ff5df21ef

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[galaxyproject/galaxy] d7c6f3: Increase release delta to 4 months ahead of 17.05.
by GitHub 06 Dec '16

06 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d7c6f39a9eb8b117c1fe8f98af1aa3bb527be953 https://github.com/galaxyproject/galaxy/commit/d7c6f39a9eb8b117c1fe8f98af1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Increase release delta to 4 months ahead of 17.05. Commit: 45afe7aa61478d88b7b99c08429f4012328247d1 https://github.com/galaxyproject/galaxy/commit/45afe7aa61478d88b7b99c08429f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- fix typo Commit: cd1ae6b9d26ac3bbb83adcfc0c058221df43ac5a https://github.com/galaxyproject/galaxy/commit/cd1ae6b9d26ac3bbb83adcfc0c05… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3271 from jmchilton/increase_release_timing Increase release delta to 4 months ahead of 17.05. Compare: https://github.com/galaxyproject/galaxy/compare/328f9d1ba0bf...cd1ae6b9d26a

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