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159 Commits
Author SHA1 Message Date
Nicola Soranzo e3b1fc1bef Merge pull request #1698 from jmchilton/ross 
[PROCEDURES] Drop Ross from the committers group.
 2016-02-17 17:36:42 +00:00
John Chilton b2da133e07 [PROCEDURES] Add Marius van den Beek to Galaxy committer group. 
Marius has been an indispensable member of the Galaxy community for a while - his contributions to tools, planemo, and ansible roles have been signficant and invaluable.

However over the last several months he has taken a very active role on the Galaxy central code base itself. He has worked through a number of very intricate bugs to tool shed, tooling, and workflow code - consistently providing high quality and important bug fixes. Beyond that he has made signficant enhancements to the testing of Galaxy and workflow available to tool developers leveraging local tool sheds. He also is very active in the review of issues and pull requests, perhaps the most important role of Galaxy committer group members.
 2016-02-08 18:47:48 +00:00
John Chilton 80f4a5eaed [PROCEDURES] Drop Ross from the committers group. 
Ross Lazarus has done a lot for Galaxy for a long time and has been a fantastic presence in the community. He is now retired and has no intention of touching the code or reviewing pull requests so I think it is best to remove him from the committers list. I have contacted him to confirm this and he has no problem with his removal from this group.

Just to reiterate, this isn't a condemnation of any kind, from the organization policies - "Periodically, active members may review this group and request inactive members are removed - this should not be interpreted as a condemnation of these inactive members but merely as a reflection of a desire to keep this group focused enough to remain effective."
 2016-02-08 18:37:21 +00:00
Martin Cech 308402235f Merge release_16.01 into dev 2016-02-08 11:54:01 -05:00
Nate Coraor 9c7c75b766 Typo 2016-02-05 09:45:30 -05:00
Nate Coraor 4b24d95f6f Improve documentation about binary-compatibility.cfg. Resolves #1672. 2016-02-04 11:07:31 -05:00
Nicola Soranzo 670a5f2c85 Merge branch 'release_16.01' into dev 2016-01-28 19:00:04 +00:00
Nate Coraor 33ba1face9 Link from the 16.01 announcement to the Admin wheels documentation, 
document the process of adding new wheels.
 2016-01-28 13:13:09 -05:00
Martin Cech f499ec0cab Merge pull request #1585 from jmchilton/16.01_release_notes 
[16.01] Release notes for 16.01
 2016-01-28 10:30:33 -05:00
John Chilton a2887dfe18 Merge 16.01 into dev. 2016-01-28 10:52:22 +00:00
Nicola Soranzo 30dcd0e39f Merge branch 'release_16.01' into dev 2016-01-27 12:02:01 +00:00
Nate Coraor 168f453094 Suggest installing virtualenv from brew 2016-01-26 16:49:39 -05:00
Nate Coraor 9827f32775 conda-requirements.txt renamed to conda-environment.txt 2016-01-26 16:48:38 -05:00
Nate Coraor dc801dc1f6 Add admin documentation for framework dependencies (wheels) for the 
16.01 release.
 2016-01-26 16:17:49 -05:00
Nicola Soranzo 08fbd8923a Merge some entries. Add some missing PRs. 2016-01-26 20:51:43 +00:00
Nicola Soranzo 281a53d975 Small RST fixes. 2016-01-26 20:03:34 +00:00
Martin Cech d1dcf25f57 add plural form 2016-01-26 13:11:24 -05:00
John Chilton 6c487941d2 Adjust tooling language based on note from @nsoranzo. 2016-01-26 11:58:29 +00:00
John Chilton 79dfff4d65 Typo discovered by @nsoranzo 2016-01-26 11:53:03 +00:00
Martin Cech f0b5f7757e add link to Main tour; add sentence to WF nesting 2016-01-26 11:15:36 -05:00
John Chilton 4064bbf94f 16.01 release notes. 2016-01-26 10:22:39 +00:00
John Chilton 528f80e40b Auto-generate 16.01 release notes. 2016-01-26 10:03:08 +00:00
John Chilton 53c699a4c3 Add note about how to modify labels in Galaxy project. 2016-01-25 15:37:21 +00:00
John Chilton 20f6bce375 New areas. 2016-01-25 15:35:56 +00:00
John Chilton 55635bff82 Update `area/` list to reflect current areas. 2016-01-25 15:27:43 +00:00
Dave B 2f760a2e6d Fix formatting. 2016-01-06 16:33:20 -05:00
Björn Grüning 016fd38e72 Merge pull request #1148 from markiskander/bcfgz_to_bcf_converter 
Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type
 2016-01-06 11:48:33 +01:00
John Chilton 1148081435 Implement a conda dependency resolver. 
Much more information on planemo PR that I used to build a test bed for this:

https://github.com/galaxyproject/planemo/pull/392

Also syncs galaxy with planemo shared library changed.
 2015-12-26 22:46:28 +00:00
John Chilton 6580d51293 Merge pull request #1296 from pvanheus/env-modules-resolve 
Documentation for dependency resolvers
 2015-12-11 15:00:19 -05:00
Peter van Heusden 73b6fb23db * Replaced all references to "version number" with "version string" 2015-12-11 20:53:00 +02:00
Peter van Heusden 035f1b5d66 * Incorporate documentation fixes from nsoranzo 
* Replace {} and .format with %s and % to preserve Python 2.6 compatibility
    * Add a modulepath= paranter to the fake resolver (Bunch object) used to test the modules dependency resolver
 2015-12-11 20:43:03 +02:00
Peter van Heusden 584d886b5e * Mention modulepath attribute in dependency resolver docs 
* Use modulepath in both environment modules resolvers
* Export MODULEPATH in generated shell command
* Add logging for operation of dependency resolvers
 2015-12-11 20:06:13 +02:00
Peter van Heusden e40fbe5374 * Add comment about base_path in sample config 
* Add documentation on dependency resolvers
 2015-12-11 07:31:10 +02:00
Eric Rasche 7cf98d32d8 Align opinions with @jmchilton 2015-12-04 13:36:01 -06:00
Eric Rasche a0c7d87db3 Ease the grunt uglify process 2015-12-04 12:09:40 -06:00
Nicola Soranzo 3524476bc6 Merge branch 'master' into dev 2015-12-01 11:42:16 +00:00
Martin Cech 5bd898118f deprecate TS direct hg api 2015-11-30 14:35:45 -05:00
Nicola Soranzo 4f6aad473d Merge branch 'master' into dev 2015-11-25 16:18:37 +00:00
Mark Iskander 825a20ef81 Modified more names, added bcf_bgzip to datatypes, added converters going both ways 2015-11-20 13:49:04 -06:00
Mark Iskander 6cd550e0c7 Added the bcf_bgzip_to_bcf converter to datatype.converters.rst, renamed files to follow standard naming scheme 2015-11-20 12:25:00 -06:00
Dannon Baker a5aeea0685 Slight wording tweak 2015-11-20 11:56:27 -05:00
Martin Cech e9ed5bfa62 clarify the bitbucket support 2015-11-20 11:45:58 -05:00
Martin Cech 76fc6becd6 add text highlights 2015-11-20 10:30:04 -05:00
Martin Cech cf16e2c7d3 add bitbucker deprecation notice 2015-11-20 10:27:59 -05:00
Nate Coraor 72faca1a3a Document GIE proxy config for nginx, mention the Ansible role. 2015-11-18 14:15:40 -05:00
Nicola Soranzo 13eb47e789 Merge pull request #1020 from dannon/issue_procedure 
[PROCEDURES] Issue procedure linkage
 2015-11-16 15:10:24 +00:00
Nicola Soranzo 3c7082c64a Fix doc/source/lib using "sphinx-apidoc -M -f -o doc/source/lib/ lib/" 2015-10-26 19:29:13 +00:00
Dannon Baker 9bbb3b97bd Fix link from org to issues. 2015-10-23 09:28:23 -04:00
Dannon Baker bc217b6a27 Place correctly after the last section. 2015-10-22 15:26:12 -04:00
Dannon Baker daf505eacc Point organization document to issue handling for binding procedure 2015-10-22 15:04:39 -04:00