- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e5a1ca: unicodify time on shed counter
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: e5a1cabe8e4268813bf20156690202973fb07207 https://github.com/galaxyproject/galaxy/commit/e5a1cabe8e4268813bf201566902… Author: Martin Cech <cech.marten(a)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/992cd51ac3aaa284478813196ef8… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/fad13d50c344...992cd51ac3aa

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[galaxyproject/usegalaxy-playbook] 686959: merge upstream disposable domains list
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/upstream-merge Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6869590f32208080f61dc800ffcdeb56530b8d8d https://github.com/galaxyproject/usegalaxy-playbook/commit/6869590f32208080… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M files/galaxy/common/config/disposable_email_blacklist.conf Log Message: ----------- merge upstream disposable domains list

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[galaxyproject/usegalaxy-playbook] 98a878: move the disposable_blacklist out of secret vars. ...
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 98a878e0e3b630a7de10dce7c656bae97dda466d https://github.com/galaxyproject/usegalaxy-playbook/commit/98a878e0e3b630a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: A files/galaxy/common/config/disposable_email_blacklist.conf A files/galaxy/test.galaxyproject.org/config/disposable_email_blacklist.conf A files/galaxy/usegalaxy.org/config/disposable_email_blacklist.conf M production/group_vars/galaxyservers.yml M production/secret_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml R templates/galaxy/common/config/disposable_email_blacklist.conf.j2 R templates/galaxy/test.galaxyproject.org/config/disposable_email_blacklist.c… R templates/galaxy/usegalaxy.org/config/disposable_email_blacklist.conf.j2 Log Message: ----------- move the disposable_blacklist out of secret vars. closes #20

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[galaxyproject/galaxy] 8b67dd: Acquire lock before attempting to install conda
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 8b67ddfa37f82081791bcca5330983a2dd1301f9 https://github.com/galaxyproject/galaxy/commit/8b67ddfa37f82081791bcca53309… Author: Marius van den Beek <m.vandenbeek(a)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/a2f234d5661f88263e1e6c5e8ede… Author: Marius van den Beek <m.vandenbeek(a)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/e9d81500caa3526200b204270aca… Author: Bjoern Gruening <bjoern.gruening(a)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/fad13d50c344112c8ab637e3c568… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/3248b679ac91...fad13d50c344

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[galaxyproject/galaxy] ffef28: shorten Conda environment names
by GitHub 24 Aug '16

24 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ffef288e4fd85261d4bd4c3e8c3abd3450fca859 https://github.com/galaxyproject/galaxy/commit/ffef288e4fd85261d4bd4c3e8c3a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- shorten Conda environment names Commit: 7ac7e48ca86c8869fc3db7361fedd1fedd1c03ca https://github.com/galaxyproject/galaxy/commit/7ac7e48ca86c8869fc3db7361fed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2794 from bgruening/shorten_conda_envs shorten Conda environment names Compare: https://github.com/galaxyproject/galaxy/compare/57937933fb97...7ac7e48ca86c

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[galaxyproject/galaxy] af9489: Acquire lock before attempting to install conda
by GitHub 24 Aug '16

24 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: af948913607b400c6b58dee701a8a23815601b81 https://github.com/galaxyproject/galaxy/commit/af948913607b400c6b58dee701a8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Acquire lock before attempting to install conda Commit: 84f309a03dd8c20076d81b6137acacc515be7721 https://github.com/galaxyproject/galaxy/commit/84f309a03dd8c20076d81b6137ac… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-22 (Mon, 22 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: 57937933fb97e17beee0711d69040e7d0efad180 https://github.com/galaxyproject/galaxy/commit/57937933fb97e17beee0711d6904… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2826 from mvdbeek/lock_conda Acquire lock before attempting to install conda Compare: https://github.com/galaxyproject/galaxy/compare/2a92a7de86a7...57937933fb97

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[galaxyproject/galaxy] 732649: improve conda doc to include TOC
by GitHub 24 Aug '16

24 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 7326498335804560d0376c555524b096c69720ce https://github.com/galaxyproject/galaxy/commit/7326498335804560d0376c555524… Author: Martin Cech <cech.marten(a)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: 3248b679ac91fbb2275fd3cd47d2fb2ea96e5a2e https://github.com/galaxyproject/galaxy/commit/3248b679ac91fbb2275fd3cd47d2… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/df47bd200736...3248b679ac91

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[galaxyproject/galaxy] f47ea8: initial curated release notes for 16.07
by GitHub 24 Aug '16

24 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: f47ea88c236be2414d40ef933dd3ee3c5aa2cbcb https://github.com/galaxyproject/galaxy/commit/f47ea88c236be2414d40ef933dd3… Author: Martin Cech <cech.marten(a)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: 53570e471e087fc92e0ef4befdd965703e4aeb14 https://github.com/galaxyproject/galaxy/commit/53570e471e087fc92e0ef4befdd9… Author: Nicola Soranzo <nicola.soranzo(a)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/96bdde85bf259c2c821a7bbacc1c… Author: Martin Cech <cech.marten(a)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/113999e5d574b29e1c197bcfe1bd… Author: John Chilton <jmchilton(a)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/c82719f22d3d8971055fc9b833dc… Author: Martin Cech <cech.marten(a)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/9b96d9dbfa875375bc172451fb9c… Author: John Chilton <jmchilton(a)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/e1060bd18fcf1bc69e5cd41f44ad… Author: John Chilton <jmchilton(a)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/04370845451da1cf839d75366d13… Author: John Chilton <jmchilton(a)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/8f571bae7129b4ce07739ab8e4d9… Author: John Chilton <jmchilton(a)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/f0ffa9c5947674d8e8731f36f00e… Author: Martin Cech <cech.marten(a)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/3d4300e5429b2b09b92cf5d9f555… Author: Martin Cech <cech.marten(a)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/26ceef668c57c0ef44f4072d3550… Author: Martin Cech <cech.marten(a)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: 08b2bda13bd4622d9e492aaa256d7c9bba5790aa https://github.com/galaxyproject/galaxy/commit/08b2bda13bd4622d9e492aaa256d… Author: Martin Cech <cech.marten(a)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/df47bd2007365f22921375fd0eb7… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/124d546be6e7...df47bd200736

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[galaxyproject/galaxy] 91de2d: Remove enable_beta_tool_command_isolation config o...
by GitHub 24 Aug '16

24 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 91de2d3681c38bc6d02180bac6d6b7ccd06482af https://github.com/galaxyproject/galaxy/commit/91de2d3681c38bc6d02180bac6d6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py Log Message: ----------- Remove enable_beta_tool_command_isolation config option Also fix import order and Python3 compatibility for lib/galaxy/jobs/__init__.py Commit: 7b65a6c41082c4a0160dba97406f9f8ae2f5edf4 https://github.com/galaxyproject/galaxy/commit/7b65a6c41082c4a0160dba97406f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix typos in config/galaxy.ini.sample Commit: 2a92a7de86a7e8afc94eaea582dfa5f298e3ce02 https://github.com/galaxyproject/galaxy/commit/2a92a7de86a7e8afc94eaea582df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #2830 from nsoranzo/remove_enable_beta_tool_command_isolation Remove enable_beta_tool_command_isolation config option Compare: https://github.com/galaxyproject/galaxy/compare/52e6c9ac3073...2a92a7de86a7

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[galaxyproject/galaxy] aa41a7: Fix tabular renderer display when total_cols > lin...
by GitHub 24 Aug '16

24 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa41a70011dfcda6cf778346dbf698ded8f827c6 https://github.com/galaxyproject/galaxy/commit/aa41a70011dfcda6cf778346dbf6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M static/maps/mvc/dataset/data.js.map 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 static/scripts/mvc/dataset/data.js Log Message: ----------- Fix tabular renderer display when total_cols > line_cols > 1 Commit: 52e6c9ac307370e0d37681a2a50a2faba3d14103 https://github.com/galaxyproject/galaxy/commit/52e6c9ac307370e0d37681a2a50a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M static/maps/mvc/dataset/data.js.map 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 static/scripts/mvc/dataset/data.js Log Message: ----------- Merge pull request #2845 from dannon/tabular_dataset_render Fix tabular renderer display when total_cols > line_cols > 1 Compare: https://github.com/galaxyproject/galaxy/compare/93e74ca51d6b...52e6c9ac3073

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