Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy 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: 99fca272708ac07bb6bc3b3b649865249c3a6f04 https://github.com/galaxyproject/galaxy/commit/99fca272708ac07bb6bc3b3b64986... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-25 (Thu, 25 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 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 M lib/galaxy/tools/deps/conda_util.py M templates/webapps/tool_shed/index.mako Log Message: ----------- Merge branch 'release_16.07' into dev 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: a14882f8720ce9eedb3119c5ae16d177018e918e https://github.com/galaxyproject/galaxy/commit/a14882f8720ce9eedb3119c5ae16d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7ac7e48ca86c...a14882f8720c