opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 02:04:04 +08:00
Code Issues Packages Projects Releases Wiki Activity
22,508 Commits 62 Branches 243 Tags
92aff618cb435f2b4d5805378e4bbcd67ae1f7a4
Commit Graph
22508 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Daniel Blankenberg 92aff618cb Fix for redirecting a non-user when a tool has require_login=True. 2016-04-15 16:39:23 -04:00
Dannon Baker 1c38b9723c Merge 16.01->16.04 2016-04-15 11:39:07 -04:00
Dannon Baker 9e278de395 Rebuild client. 2016-04-15 11:33:19 -04:00
Dannon Baker 3e79a574be Merge #2167 manually to resolve conflicts. 2016-04-15 11:31:58 -04:00
Martin Cech 8e72b3095b Merge pull request #2174 from mvdbeek/reorder_job_template 
[16.01] Backport #2146 #2145
 2016-04-15 09:59:38 -04:00
Marius van den Beek 434321915a Use "$NCPUS" if defined to set GALAXY_SLOTS 
On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the
hostname of the nodes the task runs on. But we do have "$NCPUS" with the
correct number of CPUS.
 2016-04-15 10:51:11 +02:00
Marius van den Beek e193e46e30 Place $headers before integrity_check 
PBS needs the resource selection (which will be filled in using $headers) to
appear before anything else (except the shebang), so this changes the order.
 2016-04-15 10:48:10 +02:00
Nicola Soranzo 7488e3b7be Merge branch 'release_16.01' into release_16.04 
Conflicts:
	lib/galaxy/web/framework/helpers/grids.py
 2016-04-15 09:45:32 +01:00
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
Dannon Baker 18c00899a3 Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135 
[16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters
 2016-04-14 17:20:23 -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
carlfeberhard 03c8573731 Multi-history: open rerun button in new tab 2016-04-14 12:12:23 -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
Nicola Soranzo cde04ad52d markupsafe.escape() in Python2 does not work on str containing non-ASCII characters. 
Fix #2135.
 2016-04-12 15:52:01 +01:00
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