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Author SHA1 Message Date
John Chilton 7f101b8da8 Merge pull request #2166 from blankenberg/release_16.04 
[16.04] Fix grouping tool and enhance performance when removing lines.
 2016-04-14 20:13:46 -04:00
carlfeberhard 8b49814859 Merge 16.01 into 16.04 2016-04-14 14:49:07 -04:00
Dannon Baker 68ce6ce49c Merge pull request #2169 from carlfeberhard/release_16.01 
[16.01] Merge 15.10 with 16.01
 2016-04-14 14:41:07 -04:00
carlfeberhard 570baa5bb6 Fix bad merge: when HTTP_GX_SECRET is None 2016-04-14 14:06:13 -04:00
carlfeberhard e26bff23ed Merge 'release_15.10' with 'release_16.01' 2016-04-14 12:59:05 -04:00
Daniel Blankenberg 34900f87f5 Fix grouping tool broken in 7347d75a4a / fd85979a86, and enhance performance when removing lines. 2016-04-14 12:00:11 -04:00
John Chilton f013cf2021 Merge pull request #2164 from natefoo/release_16.04 
[16.04] Fix missing pulsar-galaxy-lib update
 2016-04-14 10:46:32 -04:00
Nate Coraor 84ef4fd99f Update pulsar-galaxy-lib in pinned-requirements.txt (it was already 
updated in requirements.txt).
 2016-04-14 10:09:26 -04:00
Nate Coraor 9bb5978d53 Merge pull request #2156 from guerler/fix_data_001 
[16.04] Add tool parameters back to parameters and expose for certain tools
 2016-04-14 09:56:29 -04:00
Dannon Baker 5be5ba7531 Merge pull request #2161 from guerler/fix_wrapper_issue_001 
[16.04] Fix wrapper issue, overload __ne__
 2016-04-14 09:30:02 -04:00
guerler a889e19af7 Fix parameter wrapping 2016-04-14 07:23:06 -04:00
Nicola Soranzo c0d65092fb Merge pull request #2154 from martenson/port-middleware-fix 
[16.01] Port middleware fix
 2016-04-14 10:52:46 +01:00
guerler ac14139714 Add blank line 2016-04-13 15:50:44 -04:00
guerler 82e9ce827c Add tool parameters back to parameters 2016-04-13 15:34:11 -04:00
Martin Cech f85aaa4a27 port of middleware fix for TS (#2106) 2016-04-13 15:22:35 -04:00
Dannon Baker d5cc357170 Merge pull request #2150 from martenson/merge01to04 
[16.04] Merge 16.01 to 16.04
 2016-04-13 15:13:32 -04:00
Martin Cech 090e0d3356 Merge branch 'release_16.01' into merge01to04 2016-04-13 15:07:42 -04:00
Martin Cech 4c2bca5117 Merge pull request #2141 from martenson/fix-sideeffect 
[16.01] fix the value passed to Masthead as options were options.config before
 2016-04-13 15:05:50 -04:00
Martin Cech 87dbfeeabd Merge branch 'release_16.01' into release_16.04 
Conflicts:
	static/scripts/bundled/analysis.bundled.js
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
 2016-04-13 11:55:16 -04:00
Martin Cech 1e3b3a1558 fix the value passed to Masthead as options were options.config before 2016-04-12 14:43:18 -04:00
carlfeberhard ad952a4b8d Merge pull request #2139 from martenson/fix-inactivity 
[16.01] load options from config, not from options
 2016-04-12 13:42:37 -04:00
Martin Cech 2ebe940510 load options from config, not from options 2016-04-12 12:50:18 -04:00
Nate Coraor f03c037556 Merge pull request #2122 from jmchilton/pulsar_metadata 
[16.04] Rev Pulsar to 0.7.0.dev3.
 2016-04-12 09:01:27 -04:00
John Chilton ceeb01d84e Merge pull request #2133 from nsoranzo/release_16.04_fix_for_2093 
[16.04] Fixes due to #2093 and #2018
 2016-04-11 22:06:01 -04:00
Nicola Soranzo a9d675f5e8 Fix sys.path.insert() after #2093. 2016-04-11 20:27:25 +01:00
Nicola Soranzo 27f418c52d Remove scripts which depend on install_and_test_tool_shed_repositories. 2016-04-11 20:27:25 +01:00
Nicola Soranzo 6317297cad Merge branch 'release_16.01' into release_16.04 2016-04-11 20:24:46 +01:00
Nicola Soranzo 5f01cddc4b Merge pull request #2131 from nturaga/16.04_toolshed_fix 
[16.04] change run_tool_shed.py to see the file in the correct lcoation
 2016-04-11 20:20:38 +01:00
nitesh1989 f2bd242a2c change run_tool_shed.py to see the file in the correct lcoation 2016-04-11 13:44:51 -04:00
Nicola Soranzo fe4afefc42 Merge pull request #2114 from martenson/planemo-mention 
[16.01] mention planemo in the error message for disabled TS pushing
 2016-04-11 18:20:15 +01:00
Martin Cech f759961a29 mention planemo in the error message for disabled TS pushing 
rephrase to Norwegian
 2016-04-11 12:56:42 -04:00
John Chilton 84ad9c2ee2 Rev Pulsar to 0.7.0.dev3. 
- Fixes numerous problems mostly notably fixes external metadata generation and job metrics collection for recent Pulsar. This was broken when tools were given clean working directory.
 - Produce a new message if an older Pulsar version is targetted via REST of library (should help with upgrading to Galaxy 16.04).
 - Newer pulsar lib allows more flexible configuration of managers - update documntation to reflect this.
 2016-04-10 23:54:02 -04:00
Martin Cech abca525bee Merge pull request #2118 from jmchilton/version-16.04 
[16.04] Update version to 16.04.rc1
 2016-04-08 17:07:04 -04:00
Martin Cech f377d069e2 Merge pull request #2115 from jmchilton/dev-merge 
Merge release into latest dev.
 2016-04-08 14:29:18 -04:00
John Chilton 579846fdfb Update version to 16.04.rc1 2016-04-08 13:59:37 -04:00
John Chilton 0945809099 Merge remote-tracking branch 'upstream/release_16.01' into dev 2016-04-08 13:22:03 -04:00
John Chilton ce27863086 Merge pull request #2099 from davebx/shed_model_trim 
Consolidate duplicated method in tool_shed/model.
 2016-04-08 13:21:59 -04:00
John Chilton 0d616af28a Merge pull request #2106 from davebx/hg_middleware 
Workaround for the toolshed's hgweb.
 2016-04-08 13:20:22 -04:00
John Chilton 6f6554ea8c Merge pull request #2104 from Christian-B/unlinked_depenency_resolver_update_to_new_dependency 
Updated to Dependency change in b167a741a4
 2016-04-08 13:18:26 -04:00
John Chilton f0272e02f7 Merge pull request #2109 from mvdbeek/fix_debian_init_script 
Update debian init script
 2016-04-08 13:18:03 -04:00
Dave Bouvier 5ead1c089f Remove refactoring that belongs in a different PR. 2016-04-08 12:38:56 -04:00
Nicola Soranzo 4c7f187b35 Merge pull request #2110 from jmchilton/remove_stray_prints 
galaxy-lib tweaks
 2016-04-08 17:13:15 +01:00
Marius van den Beek d6a7acab99 Update debian init script 
to include instructions for starting galaxy >= 16.01.
 2016-04-08 16:55:45 +02:00
John Chilton 0414c2628a Expand PY3 linting to include another galaxy-lib module. 2016-04-08 10:31:39 -04:00
John Chilton be10253b69 Remove stray print statements. 
Not Python 3 compat.
 2016-04-08 10:28:09 -04:00
John Chilton 2744d5541f Merge pull request #2093 from davebx/move_scripts 
Move scripts out of lib/tool_shed.
 2016-04-08 09:54:44 -04:00
John Chilton ef604a75e5 Merge pull request #2102 from natefoo/global-drmaa-session 
Convert the DRMAA runner to use Pulsar's DRMAA session wrapper
 2016-04-08 09:47:24 -04:00
John Chilton 87ff0e38fa Merge pull request #2105 from guerler/fix_data_type_000 
Fix datatype list in workflow editor
 2016-04-08 09:45:50 -04:00
John Chilton 40953369e6 Merge pull request #2107 from ThomasWollmann/master 
Fix cli runner: use embed_metadata_in_job parameter
 2016-04-08 09:44:53 -04:00
Thomas Wollmann fb26d27b97 fixed lint error 2016-04-08 13:48:13 +02:00