Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: 9b3c061addb4f3e61d72465cf492396b9e07464e
https://github.com/galaxyproject/galaxy/commit/9b3c061addb4f3e61d72465cf492…
Author: Dave B <dave(a)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
Conflicts:
lib/galaxy/webapps/tool_shed/controllers/repository.py
Commit: a78b8bcd2aa02abf787f0974fe567ab4f70f41a1
https://github.com/galaxyproject/galaxy/commit/a78b8bcd2aa02abf787f0974fe56…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/managers/rbac_secured.py
M test/unit/managers/test_DatasetManager.py
Log Message:
-----------
Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04
Commit: c06f8c29968971c6c1e0dfc6847b3baf755f3a96
https://github.com/galaxyproject/galaxy/commit/c06f8c29968971c6c1e0dfc6847b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/model/__init__.py
Log Message:
-----------
correct the method call
Commit: 5e7ee28e0d6937fa53f39b350e04357b554ce9ae
https://github.com/galaxyproject/galaxy/commit/5e7ee28e0d6937fa53f39b350e04…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
bump freebayes in test (since it was updated)
Commit: 45e6949eeae88c0d3c4c3f6341ddc5695d329bb2
https://github.com/galaxyproject/galaxy/commit/45e6949eeae88c0d3c4c3f6341dd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-23 (Fri, 23 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
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
Merge pull request #2959 from martenson/release_16.04
[16.04] backport of model tool dependencies fix
Compare: https://github.com/galaxyproject/galaxy/compare/b748250193a2...45e6949eeae8
Branch: refs/heads/master-toolshed
Home: https://github.com/galaxyproject/galaxy
Commit: 510290feea4bb328566770b636f9f093d00e93b0
https://github.com/galaxyproject/galaxy/commit/510290feea4bb328566770b636f9…
Author: John Chilton <jmchilton(a)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/88d02dba6e851f0f60758a575920…
Author: John Chilton <jmchilton(a)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/0110d5a05a4b1b357a3f321471fc…
Author: John Chilton <jmchilton(a)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/e06cf9a97802d4c6a2ab97d973a3…
Author: John Chilton <jmchilton(a)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/d1c58f7ab039cc457d7e3fc97857…
Author: Marius van den Beek <m.vandenbeek(a)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/bf9a15389ef32de5ef09cc35876c…
Author: carlfeberhard <carlfeberhard(a)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:
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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/c3d7ca8eef014eb019493dbf06c2…
Author: Nate Coraor <nate(a)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/30d5b45d43c483c12390900a43d1…
Author: Dannon Baker <dannon.baker(a)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/6c2468832bdfbfa470596d2ae86f…
Author: Martin Cech <cech.marten(a)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:
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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/1f69bf32e8cf3c073804d2cdbb38…
Author: Nicola Soranzo <nicola.soranzo(a)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/a134587c893f6afa6f8bab1e9df7…
Author: Dave Bouvier <dave(a)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/3492e96574eabe6d2278cb294e9f…
Author: Martin Cech <cech.marten(a)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/f4806e9dd4b8b8f1743f9f081b00…
Author: Nicola Soranzo <nicola.soranzo(a)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/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: 873f34f07953eaf194ec0338139a736d413c30c0
https://github.com/galaxyproject/galaxy/commit/873f34f07953eaf194ec0338139a…
Author: Marius van den Beek <m.vandenbeek(a)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/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: c33bf2a222a09cc7707bdf621c257e1a951f969a
https://github.com/galaxyproject/galaxy/commit/c33bf2a222a09cc7707bdf621c25…
Author: Marius van den Beek <m.vandenbeek(a)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/c6c646ead407ef29a42ff6a6de71…
Author: Eric Rasche <rasche.eric(a)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/a1b2ec386e32f9fc357cb8683603…
Author: Martin Cech <cech.marten(a)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:
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Merge pull request #2843 from erasche/chat-docs
[16.07] Document the Chat Server
Commit: 4d19755c1313e8a014f873f1b011baf4f8d59310
https://github.com/galaxyproject/galaxy/commit/4d19755c1313e8a014f873f1b011…
Author: Martin Cech <cech.marten(a)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/01a24f6560be2d6cc9c6aef43e96…
Author: Martin Cech <cech.marten(a)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/04f22b70a4ecd127e7990982c09d…
Author: Martin Cech <cech.marten(a)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/e33f8fe5b623d38ec7b27c902797…
Author: Martin Cech <cech.marten(a)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/453c98d8ad572b7d9154430f5f61…
Author: Martin Cech <cech.marten(a)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/aedfdffafedd35a1ed52aec85dd3…
Author: Martin Cech <cech.marten(a)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/e52dbde3e481a30c5980f1e0171b…
Author: Dannon Baker <dannon.baker(a)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/b4495c1a8bb3e184bf35a9ebc4e7…
Author: Martin Cech <cech.marten(a)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/3d0bf645ab03585e316d673cd6b0…
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:
-----------
fix tiny things in docs
Commit: 779c357dcac2940f9bdaacf8de5259fe632ada1c
https://github.com/galaxyproject/galaxy/commit/779c357dcac2940f9bdaacf8de52…
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:
-----------
Merge branch 'docs_conda' of https://github.com/martenson/galaxy into docs_conda
Commit: 124d546be6e789a288f19c21adb229e149e9d7d2
https://github.com/galaxyproject/galaxy/commit/124d546be6e789a288f19c21adb2…
Author: Dannon Baker <dannon.baker(a)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/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: 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
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
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
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
Commit: 4f3c44f3ad386a667f156f39d1af44bf23b7a8ab
https://github.com/galaxyproject/galaxy/commit/4f3c44f3ad386a667f156f39d1af…
Author: Nate Coraor <nate(a)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/e0aad7af47547c04013dffe3874e…
Author: John Chilton <jmchilton(a)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/6631367b7cd4f2049426f3554eef…
Author: Dannon Baker <dannon.baker(a)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/3e65a165b722740b48ece5dab36a…
Author: Martin Cech <cech.marten(a)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/c98331eddd3f8a57cedca3132497…
Author: Martin Cech <cech.marten(a)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/53a5b76ff2e47bbf821845e0d217…
Author: Martin Cech <cech.marten(a)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/e891c5755f59e8865cbee56cd4fc…
Author: Dannon Baker <dannon.baker(a)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/d1821fed475a4261c007de3627cb…
Author: Martin Cech <cech.marten(a)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/52768c0c42313c08f25ba07b47cc…
Author: Dannon Baker <dannon.baker(a)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/6724146e7d09e5c0ac4f19d96e60…
Author: John Chilton <jmchilton(a)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/c01ce21e2cdb7b229dd8ced14e4e…
Author: Martin Cech <cech.marten(a)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/91a190c6eb2f37e041575548bfae…
Author: carlfeberhard <carlfeberhard(a)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/b88035955d7a81ff43858f092924…
Author: carlfeberhard <carlfeberhard(a)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/8616c0e87c055ed8e41563625498…
Author: Marius van den Beek <m.vandenbeek(a)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/fc3dcf3b875cbadf75a1eb34ce13…
Author: carlfeberhard <carlfeberhard(a)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/9636ea1b6cb1283ef9e5d8cb210a…
Author: carlfeberhard <carlfeberhard(a)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/e7cb0ac2a19f0141336285fdd8fc…
Author: carlfeberhard <carlfeberhard(a)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/b301fd42021245f5c3c729120751…
Author: carlfeberhard <carlfeberhard(a)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/8bf7256ca8ec61a167bca1dcaafa…
Author: Martin Cech <cech.marten(a)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/b50d07d5bf128ee280eb823f9b2b…
Author: carlfeberhard <carlfeberhard(a)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/e5f4f2fab6ce44b4e98f1dc54bea…
Author: carlfeberhard <carlfeberhard(a)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/646428d73f9cbcd312ed3ff5eff8…
Author: guerler <aysam.guerler(a)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/b399c086254f35d8536c1afa9fd7…
Author: John Chilton <jmchilton(a)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/67a3cf34ca0e639791ac88e849d1…
Author: Martin Cech <cech.marten(a)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/dc5aff7e44e2b0f767b7578935d4…
Author: Anthony Bretaudeau <abretaud(a)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/c497ea534897b4c1875186961e96…
Author: Daniel Blankenberg <dan.blankenberg(a)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/1f53c32ad68235537d8f6c843d1c…
Author: Nicola Soranzo <nicola.soranzo(a)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_db…
Commit: b748250193a26ddce4010759b9a22d012d281b81
https://github.com/galaxyproject/galaxy/commit/b748250193a26ddce4010759b9a2…
Author: John Chilton <jmchilton(a)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/7627abb3856a4e757b5ed5c55ec0…
Author: Nicola Soranzo <nicola.soranzo(a)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/8b3356b869beba70820235c2d089…
Author: Nicola Soranzo <nicola.soranzo(a)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/34d60e2b27ab08a3ebc5201d1c32…
Author: Martin Cech <cech.marten(a)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/c0e8a7608351679b8ebdb7120733…
Author: Dave B <dave(a)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/673a9a3a5b556973741245f96fb1…
Author: John Chilton <jmchilton(a)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
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a8bc9d5d16244badb023a9c5097efd826b26db56
https://github.com/galaxyproject/galaxy/commit/a8bc9d5d16244badb023a9c5097e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M .gitignore
M Makefile
A doc/parse_gx_xsd.py
A doc/schema_template.md
Log Message:
-----------
XSD Generated Tool Documentation.
- Add script to generate Markdown documentation from the XSD.
- Add Makefile target to build these docs, convert to HTML, and open respectively.
Commit: bb91a10a4cc17f73a051ffec41b796290505b35d
https://github.com/galaxyproject/galaxy/commit/bb91a10a4cc17f73a051ffec41b7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M Makefile
Log Message:
-----------
modify target for tool schema html builder to use pandoc
this is @jmchilton committing as @martenson...pssst
Commit: fb56a799fd0a0823df82c9946fea70df7764a18d
https://github.com/galaxyproject/galaxy/commit/fb56a799fd0a0823df82c9946fea…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M .gitignore
M Makefile
A doc/parse_gx_xsd.py
A doc/schema_template.md
Log Message:
-----------
Merge pull request #2936 from jmchilton/xsd_docs
XSD Generated Tool Documentation.
Compare: https://github.com/galaxyproject/galaxy/compare/c81ec07c6d39...fb56a799fd0a
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: c0e8a7608351679b8ebdb71207339384161d6616
https://github.com/galaxyproject/galaxy/commit/c0e8a7608351679b8ebdb7120733…
Author: Dave B <dave(a)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
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: 61a77383f65b542430c0f0fe7079567de3cb2c0f
https://github.com/galaxyproject/infrastructure-playbook/commit/61a77383f65…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
A jetstream_common/files/slurm/launch
A jetstream_common/files/slurm/slurm.conf.elastic
A jetstream_common/files/slurm/terminate
A jetstream_common/launch.yml
A jetstream_common/playbook.yml
A jetstream_common/secret_group_vars/baseenv.yml
A jetstream_common/secret_group_vars/controllers.yml
A jetstream_common/secret_group_vars/slurmclients.yml
A jetstream_common/templates/slurm/slurm.conf.j2
A jetstream_common/templates/supervisor/pulsar.j2
A jetstream_common/terminate.yml
A jetstreamiuenv/files
R jetstreamiuenv/files/slurm/launch
R jetstreamiuenv/files/slurm/slurm.conf.elastic
R jetstreamiuenv/files/slurm/terminate
M jetstreamiuenv/group_vars/slurmclients.yml
R jetstreamiuenv/launch.yml
M jetstreamiuenv/playbook.yml
A jetstreamiuenv/secret_group_vars
R jetstreamiuenv/secret_group_vars/baseenv.yml
R jetstreamiuenv/secret_group_vars/controllers.yml
R jetstreamiuenv/secret_group_vars/slurmclients.yml
A jetstreamiuenv/templates
R jetstreamiuenv/templates/slurm/slurm.conf.j2
R jetstreamiuenv/templates/supervisor/pulsar.j2
R jetstreamiuenv/terminate.yml
M jetstreamtaccenv/group_vars/slurmclients.yml
M jetstreamtaccenv/playbook.yml
A jetstreamtaccenv/secret_group_vars
R jetstreamtaccenv/secret_group_vars/baseenv.yml
R jetstreamtaccenv/secret_group_vars/controllers.yml
R jetstreamtaccenv/secret_group_vars/slurmclients.yml
A jetstreamtaccenv/templates
R jetstreamtaccenv/templates/slurm/slurm.conf.j2
R jetstreamtaccenv/templates/supervisor/pulsar.j2
Log Message:
-----------
Deduplicate Jetstream environments
Commit: 95e35c857626c84511573568c16475c01f905e78
https://github.com/galaxyproject/infrastructure-playbook/commit/95e35c85762…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M jetstream_common/playbook.yml
A jetstream_common/templates/etc/hosts.j2
M jetstream_common/templates/slurm/slurm.conf.j2
M jetstreamiuenv/group_vars/slurmclients.yml
M jetstreamiuenv/inventory
M jetstreamtaccenv/group_vars/slurmclients.yml
M jetstreamtaccenv/inventory
M roles/slurm/tasks/main.yml
Log Message:
-----------
Only require adding Jetstream hosts to inventory, not to the
galaxy_nodes list ingroup_vars/ slurmclients.yml. Also generate
/etc/hosts for Jetstream
Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/fead42a8d2…