opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
21,434 Commits 69 Branches 243 Tags
68f718d53bc6bcc44c8ccbe14c79a9fb79c3b9fc
Commit Graph
21434 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Martin Cech 68f718d53b Merge pull request #2767 from nsoranzo/release_16.01_handle_complex_repository_dependency_for_package 
[16.01] Fix misplaced parenthesis
 2016-08-10 11:05:05 -04:00
Nicola Soranzo f4cb63d6f2 Pin flake8 version 
Do not pin when forward-merging to dev branch.
Also ignore .tox/ and eggs/ as in #2650 .
 2016-08-10 15:17:21 +01:00
Nicola Soranzo 33c4025fab Fix misplaced parenthesis 
Reported by @dpryan79 in https://github.com/galaxyproject/tools-iuc/issues/906#issuecomment-238844304
 2016-08-10 14:34:08 +01:00
Dannon Baker f4631d2e59 Merge pull request #2629 from carlfeberhard/fix.saved-copy 
[16.01] UI, history: replace copy dialog on grid refresh
 2016-07-19 18:12:17 -04:00
Eric Enns 85671bd466 Fixed E302 2016-07-19 14:27:39 -04:00
Eric Enns 7e389c7d54 Fixed E226 2016-07-19 14:27:26 -04:00
Eric Enns 09b9339569 Fixed to only line_count not line_count + 1 lines and added in really basic test 2016-07-19 14:27:09 -04:00
Eric Enns 5f24afb1b3 Fix off by one error, causing only first line of file to be rendered in peek. 2016-07-19 14:26:58 -04:00
carlfeberhard bc79e9cc4a UI, history: replace copy dialog on grid refresh 
Fixes #2624

init_grid is called from update_grid to rebuild the grid. This patches
that call to replace the copy links with the dialog.

Note:
- related to #1303 which was an effort to make a single code path
for copying histories.
- Uses monkey patching to keep from porting build artifacts.
 2016-07-19 09:51:10 -04:00
Dannon Baker 67c4df712a Merge pull request #2522 from nsoranzo/release_16.01_fix_for_2479 
[16.01] Fix move_directory_files tool dependency action when destination is not empty
 2016-06-21 14:56:07 -04:00
Nicola Soranzo 89890d4f60 Fix move_directory_files tool dependency action when destination is not empty 
Historically this action moves the contents of the source directory to the
destination directory. Commit d38936bd8d
broke the install when e.g. the destination is $INSTALL_DIR, which is
created by Galaxy and is not empty (contains INSTALLATION.log after first
action).
 2016-06-21 17:59:17 +01:00
Nicola Soranzo 4bfa2f62fb Fix for py34-lint 2016-06-21 17:56:42 +01:00
Nicola Soranzo 5aaa1ecdf0 Merge pull request #2518 from dannon/backport_to_1601_pjafix 
[16.01] Copy PJAs when importing a workflow.
 2016-06-20 18:36:29 +01:00
Dannon Baker 8b2ae46467 Copy PJAs when importing a workflow. 2016-06-20 11:33:34 -04:00
Dannon Baker 75cdec9b4b Merge pull request #2479 from nsoranzo/release_16.01_fix_for_1947 
[16.01] Fix move_directory_files tool dependency action when new_file_path is on a different filesystem
 2016-06-15 10:14:32 -04:00
Martin Cech dbbf1edef3 Merge pull request #2484 from nsoranzo/release_16.01_fix_for_4a024b882f504aded1db32f1ed056f7c9109d218 
[16.01] Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries
 2016-06-10 12:06:41 -04:00
Nicola Soranzo 933f42619e Log all failed job status checks 2016-06-10 12:34:48 +01:00
Nicola Soranzo 7c40c85034 Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries 2016-06-10 12:31:00 +01:00
Nicola Soranzo d38936bd8d Move the whole directory instead of element by element 
Fix #1947.
 2016-06-09 18:41:10 +01:00
Nicola Soranzo d95e9b840d Refactor move_file() method 2016-06-09 17:59:39 +01:00
John Chilton 47a6516096 Merge pull request #2407 from carlfeberhard/fix.most_recently_used 
[16.01] API, history: fix order in most_recently_used
 2016-05-25 09:41:32 -04:00
carlfeberhard 2a29e92ef9 API, history: fix order in most_recently_used 
- Fix ascending order used in HistoryManager.most_recent to descending
- Slightly update the docs to reflect actual value better
- Add tests
 2016-05-24 17:08:08 -04:00
Dannon Baker 79dd8c82f0 Merge pull request #2312 from nsoranzo/release_16.01_fix_makos 
[16.01] Unicodify pretty datetimes which can contain non-ASCII chars
 2016-05-07 18:11:24 -04:00
John Chilton 41e6f22f33 Merge pull request #2309 from nsoranzo/release_16.01_slurm_mem_limit 
[16.01] Remove SLURM memory limit warning from stderr if the job was successful
 2016-05-05 12:47:20 -04:00
Nicola Soranzo 0f984d3bfd Unicodify pretty datetimes which can contain non-ASCII chars 2016-05-05 11:49:05 +01:00
Nicola Soranzo ad0647d677 Change elif to if because drmaa_state can be changed inside the if 2016-05-04 20:12:03 +01:00
Nicola Soranzo 338d254031 Use partial messages to match SLURM memory warnings 2016-05-04 19:56:48 +01:00
Lance Parsons 3005bba5e3 Remove SLURM memory limit warning from stderr if the job was successful 2016-05-04 16:20:39 +01:00
Dannon Baker 063b25f660 Merge pull request #2260 from jmchilton/fix_burst_background_workflows 
[16.01] Fix running workflows in the background when tool bursting is enabled.
 2016-05-03 18:18:00 -04:00
Nitesh Turaga cdea922890 Merge pull request #2195 from dannon/remoteuser_work 
[16.01] Prepass on remote user header based on maildomain and normalize confi…
 2016-05-02 14:12:33 -04:00
John Chilton 615b0b444e Fix running workflows in the background when tool bursting is enabled. 2016-04-27 15:36:45 -04:00
Dannon Baker 9e980862c8 Merge pull request #2220 from martenson/port-tstestfix 
[16.01] port TS test fix so we can rely on jenkins
 2016-04-21 15:35:17 -04:00
Martin Cech 912e6ea30f port TS test fix so we can rely on jenkins 2016-04-21 13:02:09 -04:00
Aysam Guerler 3907d83abe Merge pull request #2214 from dannon/old_library_fixes 
[16.01] Browse library date handling for non-ascii month abbreviations
 2016-04-21 11:15:51 -04:00
Dannon Baker 7e93d46239 Another location where the non-ascii month was breaking display. 2016-04-21 09:08:38 -04:00
Dannon Baker ef12ae3035 Test fix for christ-h's french language date abbreviations breaking the old library display 2016-04-21 09:00:17 -04:00
Martin Cech 5aefe1b193 Merge pull request #2207 from dannon/release_16.01 
[16.01] Rebuild client, maps were out of sync.
 2016-04-20 13:44:34 -04:00
Dannon Baker ebb49d460b Make client, somehow this got out of sync. 2016-04-20 13:19:03 -04:00
Dannon Baker 3737fc9487 Merge pull request #2198 from carlfeberhard/fix.citations-again 
[16.01] UI, citations: fix bad merge from 15.10
 2016-04-19 18:21:21 -04:00
carlfeberhard cfb8ed3269 UI, citations: fix bad merge from 15.10 
774487d created a difference between the imported name and the one
used.
 2016-04-19 15:35:15 -04:00
Dannon Baker eb15c14750 Prepass on remote user header based on maildomain and normalize config. This resolves an error reported on -dev with maildomain and user being set incorrectly. 2016-04-19 12:25:17 -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 b95cca862c always fetch new permissions as we are reusing the view 2016-04-15 12:58:36 -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
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
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