Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 510290feea4bb328566770b636f9f093d00e93b0 https://github.com/galaxyproject/galaxy/commit/510290feea4bb328566770b636f9f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add example of regressed 16.04 behavior related to dbkey output actions. Commit: 88d02dba6e851f0f60758a575920f6e7b130e261 https://github.com/galaxyproject/galaxy/commit/88d02dba6e851f0f60758a575920f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Don't fill in a cheetah default if unavailable. ... in metadata hack from #961. Commit: 0110d5a05a4b1b357a3f321471fce1b2d4960e67 https://github.com/galaxyproject/galaxy/commit/0110d5a05a4b1b357a3f321471fce... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M test/functional/tools/dbkey_output_action.xml Log Message: ----------- Add a test case to dbkey_output_action.xml. Per @nsoranzo's template and suggestion. Commit: e06cf9a97802d4c6a2ab97d973a373675e68b751 https://github.com/galaxyproject/galaxy/commit/e06cf9a97802d4c6a2ab97d973a37... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/util/template.py Log Message: ----------- Add None check to fill_template... ... as requested by @nsoranzo. Commit: d1c58f7ab039cc457d7e3fc97857cd2c314c5e5c https://github.com/galaxyproject/galaxy/commit/d1c58f7ab039cc457d7e3fc97857c... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/util/template.py A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2800 from jmchilton/dbkey_output_without_cond [16.04] Fix dbkey problem discovered by @hrhotz Commit: bf9a15389ef32de5ef09cc35876cc17154cb5a5d https://github.com/galaxyproject/galaxy/commit/bf9a15389ef32de5ef09cc35876cc... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py 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 Log Message: ----------- API, history contents: allow 'source' in payload In create, checks both kwd and payload for 'source' parameter when creating a new hdca. This allows source to be passed in the body and not query string. This fixes the copy call in history-contents when copying an hdca by drag and drop in the multi history view. Commit: c3d7ca8eef014eb019493dbf06c250c0a586b97c https://github.com/galaxyproject/galaxy/commit/c3d7ca8eef014eb019493dbf06c25... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Revert str.split() syntax for Python 2 compatibility Commit: 30d5b45d43c483c12390900a43d13fc9cb6667d5 https://github.com/galaxyproject/galaxy/commit/30d5b45d43c483c12390900a43d13... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2810 from natefoo/split-kwargs [16.07] Revert str.split() syntax for Python 2 compatibility Commit: 6c2468832bdfbfa470596d2ae86f48dc54285139 https://github.com/galaxyproject/galaxy/commit/6c2468832bdfbfa470596d2ae86f4... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py 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 Log Message: ----------- Merge pull request #2809 from carlfeberhard/fix.hdca-dnd [16.07] API, history contents: allow 'source' in payload Commit: 1f69bf32e8cf3c073804d2cdbb3823e14f1a8ce5 https://github.com/galaxyproject/galaxy/commit/1f69bf32e8cf3c073804d2cdbb382... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M run.sh Log Message: ----------- Fix run.sh --daemon Broken in commit d5c52cadfd0007338d4c89f505ff272e9acae9f9 . Partial backport from #2765 . Close #2724. Commit: a134587c893f6afa6f8bab1e9df7ff4ef74fa29c https://github.com/galaxyproject/galaxy/commit/a134587c893f6afa6f8bab1e9df7f... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Correctly check set_environment declarations when updating repository. Commit: 3492e96574eabe6d2278cb294e9fdc0fe40b283c https://github.com/galaxyproject/galaxy/commit/3492e96574eabe6d2278cb294e9fd... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py M run.sh Log Message: ----------- Merge pull request #2811 from nsoranzo/release_16.04_backports [16.04] Two backports Commit: f4806e9dd4b8b8f1743f9f081b00ef65029ea780 https://github.com/galaxyproject/galaxy/commit/f4806e9dd4b8b8f1743f9f081b00e... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/util/template.py M run.sh A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 079aeddde20fe6729c4dd721f9aa4a9855513c3f https://github.com/galaxyproject/galaxy/commit/079aeddde20fe6729c4dd721f9aa4... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/util/template.py M lib/galaxy/webapps/galaxy/api/history_contents.py 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 A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: run.sh static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/dd5411339737...079aeddde20f