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Author SHA1 Message Date
Dave Bouvier 2c8a5d9d58 Correct import order. 2016-09-23 12:13:10 -04:00
Dave Bouvier b83f0a1024 Fix whoosh indexing. 2016-09-21 14:40:12 -04:00
Martin Cech 34d60e2b27 Merge pull request #2945 from nsoranzo/release_16.07_strip_stderr 
[16.07] Strip stderr message from sacct
 2016-09-21 12:13:27 -04:00
Nicola Soranzo 8b3356b869 Strip stderr message from sacct 2016-09-21 10:02:01 +01:00
Nicola Soranzo 7627abb385 Merge branch 'release_16.04' into release_16.07 2016-09-20 15:54:19 +01:00
John Chilton b748250193 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
 2016-09-20 10:44:37 -04:00
Nicola Soranzo 1f53c32ad6 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_dbnsfp_datatypes/tabular_to_dbnsfp.py
 2016-09-19 20:51:33 +01:00
Daniel Blankenberg c497ea5348 Merge pull request #2924 from nsoranzo/release_16.07_backport_2738 
[16.07] Update python-ldap module
 2016-09-16 09:56:21 -04:00
Anthony Bretaudeau dc5aff7e44 Update python-ldap module 
Updating to the same version as galaxyproject/starforge#97
 2016-09-15 19:05:35 +01:00
Martin Cech 67a3cf34ca Merge pull request #2920 from guerler/fix_collection_refresh 
[16.07] Prevent refresh for collection selector in old run workflow form
 2016-09-15 13:19:37 -04:00
John Chilton b399c08625 Merge pull request #2918 from martenson/pick-dep-log 
[16.07] cherry pick logging the resolved dependency type
 2016-09-14 16:18:06 -04:00
guerler 646428d73f Remove change handler for data and collection multiinput selectors in old run workflow form 2016-09-14 13:53:56 -04:00
carlfeberhard e5f4f2fab6 Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 2016-09-14 13:24:52 -04:00
carlfeberhard b50d07d5bf Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 2016-09-14 13:23:41 -04:00
Martin Cech 8bf7256ca8 Merge pull request #2912 from carlfeberhard/dataset.admin-permissions 
[16.01] Allow admin to serialize/deserialize dataset permissions
 2016-09-14 13:20:00 -04:00
carlfeberhard b301fd4202 Dataset perms: correct comment 2016-09-14 13:18:46 -04:00
carlfeberhard e7cb0ac2a1 Datasets: test for anon deserialization 2016-09-13 13:10:42 -04:00
carlfeberhard 9636ea1b6c Datasets: test for anon access/manage 2016-09-13 13:09:11 -04:00
carlfeberhard fc3dcf3b87 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
 2016-09-13 13:00:58 -04:00
Marius van den Beek 8616c0e87c Log the resolved dependency type 2016-09-13 11:41:55 -04:00
carlfeberhard b88035955d Datasets: confirm admin ability to set permissions 
The power was inside you all along.
 2016-09-12 11:04:39 -04:00
carlfeberhard 91a190c6eb Datasets: allow admin to serialize permissions 
And updates tests.
 2016-09-12 10:50:57 -04:00
Martin Cech c01ce21e2c Merge pull request #2864 from jmchilton/conda_fixes 
[16.07] Fix three conda bugs.
 2016-08-26 13:19:53 -04:00
John Chilton 6724146e7d 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).
 2016-08-26 12:24:11 -04:00
Dannon Baker 52768c0c42 Merge pull request #2863 from martenson/release_16.07 
[16.07] backport disable conda_auto_init
 2016-08-26 12:23:03 -04:00
Martin Cech d1821fed47 disable conda_auto_init 2016-08-26 12:18:08 -04:00
Dannon Baker e891c5755f Merge pull request #2859 from martenson/fix-notes-include 
[16.07] fix inclusion of release notes in the announcement
 2016-08-25 15:24:33 -04:00
Martin Cech 53a5b76ff2 Merge pull request #2860 from dannon/postfork-tool-conf-watcher-test-fix 
[16.07] Unused import cleanup for #2856
 2016-08-25 14:53:22 -04:00
Martin Cech c98331eddd Merge pull request #2856 from natefoo/postfork-tool-conf-watcher-test-fix 
[16.07] Postfork tool conf watcher test fix
 2016-08-25 14:43:13 -04:00
Martin Cech 3e65a165b7 fix inclusion of release notes in announcement 2016-08-25 14:32:10 -04:00
Dannon Baker 6631367b7c Unused import, cleanup for #2856 2016-08-25 13:48:58 -04:00
John Chilton e0aad7af47 Update version to 16.07 v16.07 2016-08-25 13:41:10 -04:00
Nate Coraor 4f3c44f3ad 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.
 2016-08-25 13:23:36 -04:00
John Chilton 992cd51ac3 Merge pull request #2855 from martenson/fix-ts-unicodify 
[16.07] unicodify TS main template
 2016-08-25 12:56:23 -04:00
Martin Cech e5a1cabe8e unicodify time on shed counter 
to prevent problems with dates that contain non-ascii
 2016-08-25 11:44:00 -04:00
John Chilton fad13d50c3 Merge pull request #2851 from martenson/backport_2794_2826 
[16.07] Backport conda fixes
 2016-08-24 18:05:39 -04:00
Bjoern Gruening e9d81500ca shorten Conda environment names 2016-08-24 15:12:54 -04:00
Marius van den Beek a2f234d566 Create default tool_dependency dir if it doesn't exist 2016-08-24 15:12:44 -04:00
Marius van den Beek 8b67ddfa37 Acquire lock before attempting to install conda 2016-08-24 15:12:38 -04:00
John Chilton 3248b679ac Merge pull request #2850 from martenson/docs_conda 
[16.07] conda docs - add TOC
 2016-08-24 13:37:39 -04:00
John Chilton df47bd2007 Merge pull request #2821 from martenson/16.07_release_notes 
[16.07] curated release notes for 16.07
 2016-08-24 13:36:16 -04:00
Martin Cech 08b2bda13b change links to target official docs 2016-08-24 13:18:26 -04:00
Martin Cech 7326498335 improve conda doc to include TOC 2016-08-24 12:25:10 -04:00
Dannon Baker 124d546be6 Merge pull request #2844 from martenson/docs_conda 
[16.07] add conda docs converted and modified from IUC googledoc
 2016-08-24 11:45:28 -04:00
Martin Cech 779c357dca Merge branch 'docs_conda' of https://github.com/martenson/galaxy into docs_conda 2016-08-24 11:43:13 -04:00
Martin Cech 3d0bf645ab fix tiny things in docs 2016-08-24 11:28:32 -04:00
Martin Cech b4495c1a8b Merge pull request #17 from dannon/docs_conda 
Conda/conda standardization
 2016-08-23 20:29:07 -04:00
Dannon Baker e52dbde3e4 Conda/conda standardization 2016-08-23 17:45:56 -04:00
Martin Cech aedfdffafe add more literal includes 2016-08-23 17:41:07 -04:00
Martin Cech 453c98d8ad this one is even weirder than the ones before 2016-08-23 17:35:03 -04:00