- galaxy-commits - lists.galaxyproject.org

[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 07 Dec '16

07 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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[galaxyproject/galaxy] 142ba8: Fix tour URLs in welcome
by GitHub 06 Dec '16

06 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 142ba89a990328548ecbafb5af06ba6799950cd8 https://github.com/galaxyproject/galaxy/commit/142ba89a990328548ecbafb5af06… 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: 328f9d1ba0bf60ca8e6be706327a3ad3b0c6e656 https://github.com/galaxyproject/galaxy/commit/328f9d1ba0bf60ca8e6be706327a… 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 #3274 from dannon/fix_tour_welcome Fix tour URLs in welcome Compare: https://github.com/galaxyproject/galaxy/compare/ab52cc46ed93...328f9d1ba0bf

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[galaxyproject/galaxy] 7fa10a: Simplify dependency list for cached environemnts (...
by GitHub 06 Dec '16

06 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7fa10aa907ad6527f9e71a4d661281d21ac9150c https://github.com/galaxyproject/galaxy/commit/7fa10aa907ad6527f9e71a4d6612… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Simplify dependency list for cached environemnts (many thanks @nsoranzo) Commit: d0ad2ae1ce296e41e88264b0a770bf9c176db814 https://github.com/galaxyproject/galaxy/commit/d0ad2ae1ce296e41e88264b0a770… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3272 from mvdbeek/fix_superfluous_brackets [16.10] Simplify dependency list for cached environemnts (many thanks @nsoranzo) Commit: ab52cc46ed9365eab85881abfcb196b1e2fca63d https://github.com/galaxyproject/galaxy/commit/ab52cc46ed9365eab85881abfcb1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/5b1b191f2ee5...ab52cc46ed93

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[galaxyproject/galaxy] 7fa10a: Simplify dependency list for cached environemnts (...
by GitHub 06 Dec '16

06 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 7fa10aa907ad6527f9e71a4d661281d21ac9150c https://github.com/galaxyproject/galaxy/commit/7fa10aa907ad6527f9e71a4d6612… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Simplify dependency list for cached environemnts (many thanks @nsoranzo) Commit: d0ad2ae1ce296e41e88264b0a770bf9c176db814 https://github.com/galaxyproject/galaxy/commit/d0ad2ae1ce296e41e88264b0a770… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3272 from mvdbeek/fix_superfluous_brackets [16.10] Simplify dependency list for cached environemnts (many thanks @nsoranzo) Compare: https://github.com/galaxyproject/galaxy/compare/622f2997376b...d0ad2ae1ce29

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[galaxyproject/galaxy] bab709: Request information about tool dependencies from t...
by GitHub 05 Dec '16

05 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bab709c755ef2ba83849c9457f9558d79a11eaf3 https://github.com/galaxyproject/galaxy/commit/bab709c755ef2ba83849c9457f95… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Request information about tool dependencies from toolshed and make available in prepare_for_install Commit: 72f417ef977030ce092219b7565f2cb6650e5a2c https://github.com/galaxyproject/galaxy/commit/72f417ef977030ce092219b7565f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Display requirement status on TS install This commit displays tool requirements as defined in the tool xml during the install confirmation dialog. If a tool dependency is defined in the tool XML, but not in a tool_dependencies.xml, a warning is shown if conda is not activated. This should close #3257. Commit: f20c478bd963c9eb907b711af659f17ef47c171f https://github.com/galaxyproject/galaxy/commit/f20c478bd963c9eb907b711af659… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Use Tool Shed instead of toolshed Commit: 622f2997376bceb30b822f6c5f1b3a0096e5e2f9 https://github.com/galaxyproject/galaxy/commit/622f2997376bceb30b822f6c5f1b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #3262 from mvdbeek/conda_only_improvements [16.10] Display tool requirements for conda-only tools Commit: 5b1b191f2ee555be0247310e1a6c303d783d9ffa https://github.com/galaxyproject/galaxy/commit/5b1b191f2ee555be0247310e1a6c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/982a35df087a...5b1b191f2ee5

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[galaxyproject/galaxy] bab709: Request information about tool dependencies from t...
by GitHub 05 Dec '16

05 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: bab709c755ef2ba83849c9457f9558d79a11eaf3 https://github.com/galaxyproject/galaxy/commit/bab709c755ef2ba83849c9457f95… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Request information about tool dependencies from toolshed and make available in prepare_for_install Commit: 72f417ef977030ce092219b7565f2cb6650e5a2c https://github.com/galaxyproject/galaxy/commit/72f417ef977030ce092219b7565f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Display requirement status on TS install This commit displays tool requirements as defined in the tool xml during the install confirmation dialog. If a tool dependency is defined in the tool XML, but not in a tool_dependencies.xml, a warning is shown if conda is not activated. This should close #3257. Commit: f20c478bd963c9eb907b711af659f17ef47c171f https://github.com/galaxyproject/galaxy/commit/f20c478bd963c9eb907b711af659… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Use Tool Shed instead of toolshed Commit: 622f2997376bceb30b822f6c5f1b3a0096e5e2f9 https://github.com/galaxyproject/galaxy/commit/622f2997376bceb30b822f6c5f1b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #3262 from mvdbeek/conda_only_improvements [16.10] Display tool requirements for conda-only tools Compare: https://github.com/galaxyproject/galaxy/compare/888a8f91537e...622f2997376b

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