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
22,530 Commits 62 Branches 243 Tags
212f7f4aabc6e859dfcbe00db2cfa36d4d2e48e8
Commit Graph
22530 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Martin Cech 212f7f4aab Merge branch 'release_16.01' into release_16.04 
Conflicts:
	client/galaxy/scripts/mvc/library/library-dataset-view.js
	static/maps/mvc/library/library-dataset-view.js.map
	static/maps/mvc/library/library-folder-view.js.map
	static/maps/mvc/library/library-library-view.js.map
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js.map
	static/scripts/mvc/library/library-dataset-view.js
	static/scripts/mvc/library/library-folder-view.js
	static/scripts/mvc/library/library-library-view.js
 2016-04-19 11:02:44 -04:00
John Chilton 00a55f8c02 Merge pull request #2190 from martenson/fix-import-libraries 
[16.04] fix a bug with missing history_id in libraries dataset import
 2016-04-19 09:14:14 -04:00
Eric Rasche e2f88296f8 Merge pull request #2176 from martenson/fix-permissions-caching 
[16.01] libraries: always fetch new permissions as we are reusing the view
 2016-04-18 21:53:52 +00:00
Martin Cech 75864e552b Merge pull request #2191 from guerler/fix_message_000 
[16.04] Fix message in legacy panel mako
 2016-04-18 17:04:31 -04:00
Martin Cech 76691ab2e1 Merge pull request #2189 from carlfeberhard/fix.published-history-long-titles-have-to-be-truncated 
[16.04] Fix.published history long titles have to be truncated
 2016-04-18 16:02:51 -04:00
Martin Cech db805184f5 Merge pull request #2184 from jmchilton/pulsar_fixes_more_v2_updated_even_more_revised_2 
[16.04] More Pulsar fixes.
 2016-04-18 16:02:11 -04:00
guerler bbd76f139b Fix message in legacy panel mako 2016-04-18 15:45:52 -04:00
Martin Cech 642fccd288 do not pass variable that is not used 2016-04-18 15:27:36 -04:00
Martin Cech 35ab333c7e remove old template 2016-04-18 15:18:50 -04:00
Martin Cech 980d37f50f fix a bug with missing history_id in libraries dataset import 
also allow creation of new histories as exists in the folderlist view
 2016-04-18 15:14:06 -04:00
carlfeberhard 5d39c84a71 UI, history/display: remove unused styles 2016-04-18 14:11:05 -04:00
carlfeberhard 9ea399694f UI, display_base: render links in header first 
This allows text to flow around them and for them to be positioned at/
near the top (and remain clickable).

This is a stop-gap/kludge and what we'd really want to do is move away
from absolutely positoned panels/layouts so elements like this can
stretch more naturally around their contents.

Fixes #2172
 2016-04-18 14:05:22 -04:00
John Chilton 53021ef33e Merge pull request #2186 from martenson/port-tstest-fix 
[16.04] Port TS push test fix
 2016-04-18 13:12:38 -04:00
Martin Cech 1fd326855d improve on refactoring of the test 2016-04-18 12:42:39 -04:00
Martin Cech a85b5ee762 remove unused import 2016-04-18 12:42:33 -04:00
Martin Cech 76386b5eab remove unwanted check 2016-04-18 12:42:24 -04:00
Martin Cech 7ad55b7eb8 try pushing again when we get unexpected exception... 2016-04-18 12:42:19 -04:00
Dannon Baker ab015c67df Merge pull request #2182 from guerler/fix_masthead_002 
[16.04] Remove redundant ui divs, move masthead into #everything
 2016-04-18 09:56:52 -04:00
guerler cea9a12238 Replace masthead dom to avoid duplication 2016-04-18 09:49:02 -04:00
John Chilton 49a7328186 More Pulsar fixes. 
- Fix working directory outputs for a2e3140375 (giving tools clean working directories).
 - Fix copy action when target directory doesn't already exist (https://github.com/galaxyproject/pulsar/pull/107 thanks to @natefoo).
 - Fix handling of Pulsar jobs that fail during submission (https://github.com/galaxyproject/pulsar/pull/103 thanks to @mvdbeek).
 - Fix PBS status reporting (https://github.com/galaxyproject/pulsar/pull/102 thanks to @mvdbeek).
 - Fix for JetStream that allows setting staging directories on a per-manager basis (https://github.com/galaxyproject/pulsar/commit/7d4030412d1aa58d0c3daa86d0ad7113c79fee81).
 2016-04-18 09:16:28 -04:00
Nicola Soranzo e1d937e430 Merge pull request #2180 from blankenberg/tool-login-required 
[16.04] Fix for redirecting a non-user when a tool has require_login=True.
 2016-04-18 11:50:23 +01:00
Daniel Blankenberg 92aff618cb Fix for redirecting a non-user when a tool has require_login=True. 2016-04-15 16:39:23 -04:00
Martin Cech b95cca862c always fetch new permissions as we are reusing the view 2016-04-15 12:58:36 -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