Branch: refs/heads/master-toolshed 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: f47ea88c236be2414d40ef933dd3ee3c5aa2cbcb https://github.com/galaxyproject/galaxy/commit/f47ea88c236be2414d40ef933dd3e... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst Log Message: ----------- initial curated release notes for 16.07 Commit: 873f34f07953eaf194ec0338139a736d413c30c0 https://github.com/galaxyproject/galaxy/commit/873f34f07953eaf194ec0338139a7... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Inject HOME, so that conda doens't attempt to write to ~/.conda Commit: 53570e471e087fc92e0ef4befdd965703e4aeb14 https://github.com/galaxyproject/galaxy/commit/53570e471e087fc92e0ef4befdd96... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Merge some entries, rephrasing and fixes Commit: 96bdde85bf259c2c821a7bbacc1c4aef60c3f3b7 https://github.com/galaxyproject/galaxy/commit/96bdde85bf259c2c821a7bbacc1c4... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07_announce.rst Log Message: ----------- add a highlight, update git commands Commit: 113999e5d574b29e1c197bcfe1bdef1777c5c507 https://github.com/galaxyproject/galaxy/commit/113999e5d574b29e1c197bcfe1bde... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Tweaks to language of many of enhancements in 16.07 release notes. Commit: c82719f22d3d8971055fc9b833dc7fd2519fad22 https://github.com/galaxyproject/galaxy/commit/c82719f22d3d8971055fc9b833dc7... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst Log Message: ----------- drop subheaders, reorder, tweak to wording Commit: 9b96d9dbfa875375bc172451fb9c7e6993c62f41 https://github.com/galaxyproject/galaxy/commit/9b96d9dbfa875375bc172451fb9c7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- More user-focused language in release notes. Commit: e1060bd18fcf1bc69e5cd41f44adde37ba55ae1d https://github.com/galaxyproject/galaxy/commit/e1060bd18fcf1bc69e5cd41f44add... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Spelling fix thanks to @nsoranzo. Commit: 04370845451da1cf839d75366d131325105698fe https://github.com/galaxyproject/galaxy/commit/04370845451da1cf839d75366d131... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Another spelling fix thanks to @nsoranzo. Commit: 8f571bae7129b4ce07739ab8e4d9ddcef020af5e https://github.com/galaxyproject/galaxy/commit/8f571bae7129b4ce07739ab8e4d9d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Wording fix thanks to @nsoranzo. Commit: f0ffa9c5947674d8e8731f36f00eb82b757b6558 https://github.com/galaxyproject/galaxy/commit/f0ffa9c5947674d8e8731f36f00eb... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- drop GRT reference Commit: 3d4300e5429b2b09b92cf5d9f55541643a0ff62b https://github.com/galaxyproject/galaxy/commit/3d4300e5429b2b09b92cf5d9f5554... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- tweak wording of notes Commit: 26ceef668c57c0ef44f4072d3550472ff9582e29 https://github.com/galaxyproject/galaxy/commit/26ceef668c57c0ef44f4072d35504... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07_announce.rst Log Message: ----------- announce conda as beta, link the IUC doc, link DTD wiki Commit: c33bf2a222a09cc7707bdf621c257e1a951f969a https://github.com/galaxyproject/galaxy/commit/c33bf2a222a09cc7707bdf621c257... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2825 from mvdbeek/conda_install_fix Inject HOME, so that conda doens't attempt to write to ~/.conda Commit: c6c646ead407ef29a42ff6a6de7182837a97a1f7 https://github.com/galaxyproject/galaxy/commit/c6c646ead407ef29a42ff6a6de718... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png M doc/source/admin/index.rst Log Message: ----------- Document the Chat Server Commit: a1b2ec386e32f9fc357cb86836033a46084d8855 https://github.com/galaxyproject/galaxy/commit/a1b2ec386e32f9fc357cb86836033... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png M doc/source/admin/index.rst Log Message: ----------- Merge pull request #2843 from erasche/chat-docs [16.07] Document the Chat Server Commit: 4d19755c1313e8a014f873f1b011baf4f8d59310 https://github.com/galaxyproject/galaxy/commit/4d19755c1313e8a014f873f1b011b... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst Log Message: ----------- add conda docs converted and modified from IUC googledoc Commit: 01a24f6560be2d6cc9c6aef43e9665f140fc3640 https://github.com/galaxyproject/galaxy/commit/01a24f6560be2d6cc9c6aef43e966... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- rst problems Commit: 04f22b70a4ecd127e7990982c09db7278bf1cf98 https://github.com/galaxyproject/galaxy/commit/04f22b70a4ecd127e7990982c09db... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- fix plural, split lines to prevent indentation Commit: e33f8fe5b623d38ec7b27c90279713a18807ee48 https://github.com/galaxyproject/galaxy/commit/e33f8fe5b623d38ec7b27c9027971... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- replace apostrophes Commit: 453c98d8ad572b7d9154430f5f61123d7ca5fbc4 https://github.com/galaxyproject/galaxy/commit/453c98d8ad572b7d9154430f5f611... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- this one is even weirder than the ones before Commit: aedfdffafedd35a1ed52aec85dd373c76b7c3135 https://github.com/galaxyproject/galaxy/commit/aedfdffafedd35a1ed52aec85dd37... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- add more literal includes Commit: e52dbde3e481a30c5980f1e0171b720c557ee72d https://github.com/galaxyproject/galaxy/commit/e52dbde3e481a30c5980f1e0171b7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Conda/conda standardization Commit: b4495c1a8bb3e184bf35a9ebc4e795b7da3aadbb https://github.com/galaxyproject/galaxy/commit/b4495c1a8bb3e184bf35a9ebc4e79... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #17 from dannon/docs_conda Conda/conda standardization Commit: 3d0bf645ab03585e316d673cd6b073e706fb616d https://github.com/galaxyproject/galaxy/commit/3d0bf645ab03585e316d673cd6b07... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- fix tiny things in docs Commit: 779c357dcac2940f9bdaacf8de5259fe632ada1c https://github.com/galaxyproject/galaxy/commit/779c357dcac2940f9bdaacf8de525... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge branch 'docs_conda' of https://github.com/martenson/galaxy into docs_conda Commit: 124d546be6e789a288f19c21adb229e149e9d7d2 https://github.com/galaxyproject/galaxy/commit/124d546be6e789a288f19c21adb22... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst Log Message: ----------- Merge pull request #2844 from martenson/docs_conda [16.07] add conda docs converted and modified from IUC googledoc Commit: 7326498335804560d0376c555524b096c69720ce https://github.com/galaxyproject/galaxy/commit/7326498335804560d0376c555524b... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- improve conda doc to include TOC Commit: 08b2bda13bd4622d9e492aaa256d7c9bba5790aa https://github.com/galaxyproject/galaxy/commit/08b2bda13bd4622d9e492aaa256d7... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M doc/source/releases/16.07_announce.rst Log Message: ----------- change links to target official docs Commit: df47bd2007365f22921375fd0eb757f0ec749473 https://github.com/galaxyproject/galaxy/commit/df47bd2007365f22921375fd0eb75... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst Log Message: ----------- Merge pull request #2821 from martenson/16.07_release_notes [16.07] curated release notes for 16.07 Commit: 3248b679ac91fbb2275fd3cd47d2fb2ea96e5a2e https://github.com/galaxyproject/galaxy/commit/3248b679ac91fbb2275fd3cd47d2f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2850 from martenson/docs_conda [16.07] conda docs - add TOC Commit: 8b67ddfa37f82081791bcca5330983a2dd1301f9 https://github.com/galaxyproject/galaxy/commit/8b67ddfa37f82081791bcca533098... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Acquire lock before attempting to install conda Commit: a2f234d5661f88263e1e6c5e8edef1e521b55359 https://github.com/galaxyproject/galaxy/commit/a2f234d5661f88263e1e6c5e8edef... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Create default tool_dependency dir if it doesn't exist Commit: e9d81500caa3526200b204270aca175839f36f56 https://github.com/galaxyproject/galaxy/commit/e9d81500caa3526200b204270aca1... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- shorten Conda environment names Commit: fad13d50c344112c8ab637e3c568e43d863730bd https://github.com/galaxyproject/galaxy/commit/fad13d50c344112c8ab637e3c568e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2851 from martenson/backport_2794_2826 [16.07] Backport conda fixes Commit: e5a1cabe8e4268813bf20156690202973fb07207 https://github.com/galaxyproject/galaxy/commit/e5a1cabe8e4268813bf2015669020... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M templates/webapps/tool_shed/index.mako Log Message: ----------- unicodify time on shed counter to prevent problems with dates that contain non-ascii Commit: 992cd51ac3aaa284478813196ef8aa0cb2c16246 https://github.com/galaxyproject/galaxy/commit/992cd51ac3aaa284478813196ef8a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M templates/webapps/tool_shed/index.mako Log Message: ----------- Merge pull request #2855 from martenson/fix-ts-unicodify [16.07] unicodify TS main template Commit: 4f3c44f3ad386a667f156f39d1af44bf23b7a8ab https://github.com/galaxyproject/galaxy/commit/4f3c44f3ad386a667f156f39d1af4... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Move the registration of the start function into the ToolConfWatcher itself so it doesn't have to be called by things that instantiate it. Fixes #2831. Commit: e0aad7af47547c04013dffe3874e757c905b2021 https://github.com/galaxyproject/galaxy/commit/e0aad7af47547c04013dffe3874e7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.07 Commit: 6631367b7cd4f2049426f3554eef6da626b83837 https://github.com/galaxyproject/galaxy/commit/6631367b7cd4f2049426f3554eef6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Unused import, cleanup for #2856 Commit: 3e65a165b722740b48ece5dab36a2a28cfa7681c https://github.com/galaxyproject/galaxy/commit/3e65a165b722740b48ece5dab36a2... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- fix inclusion of release notes in announcement Commit: c98331eddd3f8a57cedca313249798e1e45a9555 https://github.com/galaxyproject/galaxy/commit/c98331eddd3f8a57cedca31324979... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #2856 from natefoo/postfork-tool-conf-watcher-test-fix [16.07] Postfork tool conf watcher test fix Commit: 53a5b76ff2e47bbf821845e0d2170240902a70eb https://github.com/galaxyproject/galaxy/commit/53a5b76ff2e47bbf821845e0d2170... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #2860 from dannon/postfork-tool-conf-watcher-test-fix [16.07] Unused import cleanup for #2856 Commit: e891c5755f59e8865cbee56cd4fcc8e5f4bbd0af https://github.com/galaxyproject/galaxy/commit/e891c5755f59e8865cbee56cd4fcc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Merge pull request #2859 from martenson/fix-notes-include [16.07] fix inclusion of release notes in the announcement Commit: d1821fed475a4261c007de3627cb3eeb42d53a1f https://github.com/galaxyproject/galaxy/commit/d1821fed475a4261c007de3627cb3... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- disable conda_auto_init Commit: 52768c0c42313c08f25ba07b47ccf2bed28248f4 https://github.com/galaxyproject/galaxy/commit/52768c0c42313c08f25ba07b47ccf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #2863 from martenson/release_16.07 [16.07] backport disable conda_auto_init Commit: 6724146e7d09e5c0ac4f19d96e600d14831a8abe https://github.com/galaxyproject/galaxy/commit/6724146e7d09e5c0ac4f19d96e600... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix three conda bugs. - Don't attempt file lock if don't have write access for lock. - Set disabled to False if conda present and auto_init is False. - Use the correct parent path for conda_prefix (if default parent path is overridden). Commit: c01ce21e2cdb7b229dd8ced14e4e2c1c7fdf294c https://github.com/galaxyproject/galaxy/commit/c01ce21e2cdb7b229dd8ced14e4e2... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2864 from jmchilton/conda_fixes [16.07] Fix three conda bugs. Commit: 91a190c6eb2f37e041575548bfae85d61b64ce7e https://github.com/galaxyproject/galaxy/commit/91a190c6eb2f37e041575548bfae8... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: allow admin to serialize permissions And updates tests. Commit: b88035955d7a81ff43858f092924b60bef1bca9c https://github.com/galaxyproject/galaxy/commit/b88035955d7a81ff43858f092924b... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: confirm admin ability to set permissions The power was inside you all along. Commit: 8616c0e87c055ed8e41563625498818a76769b2f https://github.com/galaxyproject/galaxy/commit/8616c0e87c055ed8e415636254988... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Log the resolved dependency type Commit: fc3dcf3b875cbadf75a1eb34ce1395e29dbe0baf https://github.com/galaxyproject/galaxy/commit/fc3dcf3b875cbadf75a1eb34ce139... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Permissions, datasets: allow admin in RBAC - Admin are considered permitted when calling ** dataset_manager.permssions.access and ** dataset_manager.permissions.manage - Update bad test - Add admin test to other permission checks Commit: 9636ea1b6cb1283ef9e5d8cb210a962eff45bbef https://github.com/galaxyproject/galaxy/commit/9636ea1b6cb1283ef9e5d8cb210a9... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon access/manage Commit: e7cb0ac2a19f0141336285fdd8fcf9aeb32221f2 https://github.com/galaxyproject/galaxy/commit/e7cb0ac2a19f0141336285fdd8fcf... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon deserialization Commit: b301fd42021245f5c3c7291207510659aa66b5ac https://github.com/galaxyproject/galaxy/commit/b301fd42021245f5c3c7291207510... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- Dataset perms: correct comment Commit: 8bf7256ca8ec61a167bca1dcaafa0b83cf12fa5a https://github.com/galaxyproject/galaxy/commit/8bf7256ca8ec61a167bca1dcaafa0... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #2912 from carlfeberhard/dataset.admin-permissions [16.01] Allow admin to serialize/deserialize dataset permissions Commit: b50d07d5bf128ee280eb823f9b2b5677e549b5e5 https://github.com/galaxyproject/galaxy/commit/b50d07d5bf128ee280eb823f9b2b5... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: e5f4f2fab6ce44b4e98f1dc54bea138d1185aa85 https://github.com/galaxyproject/galaxy/commit/e5f4f2fab6ce44b4e98f1dc54bea1... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 646428d73f9cbcd312ed3ff5eff8e36ee12f213e https://github.com/galaxyproject/galaxy/commit/646428d73f9cbcd312ed3ff5eff8e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Remove change handler for data and collection multiinput selectors in old run workflow form Commit: b399c086254f35d8536c1afa9fd7a2e50ec339a9 https://github.com/galaxyproject/galaxy/commit/b399c086254f35d8536c1afa9fd7a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Merge pull request #2918 from martenson/pick-dep-log [16.07] cherry pick logging the resolved dependency type Commit: 67a3cf34ca0e639791ac88e849d120dce355d3ef https://github.com/galaxyproject/galaxy/commit/67a3cf34ca0e639791ac88e849d12... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2920 from guerler/fix_collection_refresh [16.07] Prevent refresh for collection selector in old run workflow form Commit: dc5aff7e44e2b0f767b7578935d46db7d7707066 https://github.com/galaxyproject/galaxy/commit/dc5aff7e44e2b0f767b7578935d46... Author: Anthony Bretaudeau <abretaud@irisa.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update python-ldap module Updating to the same version as galaxyproject/starforge#97 Commit: c497ea534897b4c1875186961e96da52129c4a3a https://github.com/galaxyproject/galaxy/commit/c497ea534897b4c1875186961e96d... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #2924 from nsoranzo/release_16.07_backport_2738 [16.07] Update python-ldap module Commit: 1f53c32ad68235537d8f6c843d1cd81eda5c11c3 https://github.com/galaxyproject/galaxy/commit/1f53c32ad68235537d8f6c843d1cd... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion This should have been added in https://bitbucket.org/galaxy/galaxy-central/pull-requests/640/ Actual source code comes from https://github.com/galaxyproject/tools-iuc/blob/master/datatypes/snpsift_dbn... Commit: b748250193a26ddce4010759b9a22d012d281b81 https://github.com/galaxyproject/galaxy/commit/b748250193a26ddce4010759b9a22... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge pull request #2938 from nsoranzo/release_16.04_tabular_to_dbnsfp [16.04] Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion Commit: 7627abb3856a4e757b5ed5c55ec05a4f97bd4cac https://github.com/galaxyproject/galaxy/commit/7627abb3856a4e757b5ed5c55ec05... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 8b3356b869beba70820235c2d0894cee9e590ffe https://github.com/galaxyproject/galaxy/commit/8b3356b869beba70820235c2d0894... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Strip stderr message from sacct Commit: 34d60e2b27ab08a3ebc5201d1c3282d346d40af0 https://github.com/galaxyproject/galaxy/commit/34d60e2b27ab08a3ebc5201d1c328... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2945 from nsoranzo/release_16.07_strip_stderr [16.07] Strip stderr message from sacct Commit: c0e8a7608351679b8ebdb71207339384161d6616 https://github.com/galaxyproject/galaxy/commit/c0e8a7608351679b8ebdb71207339... Author: Dave B <dave@bx.psu.edu> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py Log Message: ----------- [16.07] Fix tool dependencies handling in Tool Shed model (#2950) * Fix the cause of toolshed test 1400 failing. * Fix handling of repositories without tool dependencies. * Fix tool dependency retrieval. In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue. * Correct the logic that returns an empty string for an empty dict. * Fix getting latest revision with tool dependencies. * Use self.app instead of trans.app Commit: 673a9a3a5b556973741245f96fb15ccc30405da6 https://github.com/galaxyproject/galaxy/commit/673a9a3a5b556973741245f96fb15... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M config/galaxy.ini.sample A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/template.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M run.sh 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 templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/index.mako A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #2958 from galaxyproject/release_16.07 [master-toolshed] merge in release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/3e65e768c8cb...673a9a3a5b55