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Author SHA1 Message Date
Eric Rasche d032a1a4aa Linting 2016-06-04 15:47:57 +00:00
Eric Rasche f2941c47aa Add Galactic Radio Telescope script 2016-06-03 22:33:49 +00:00
Björn Grüning 789c300936 Merge pull request #2452 from leobiscassi/add_pdbqt_datatype 
Add support to PDBQT molecule datatype
 2016-06-03 20:36:40 +02:00
leobiscassi 6abcbb84a8 Adjust sniff function 2016-06-03 14:56:09 -03:00
leobiscassi e428a801db fix pep8 errors 2016-06-03 14:09:11 -03:00
leobiscassi c213175513 Adjust set_peek method of the pdbqt class 2016-06-03 12:56:53 -03:00
leobiscassi 2e6317e777 Add support to pdbqt datatype 2016-06-03 10:31:38 -03:00
Björn Grüning 30fd1d679b Merge pull request #2429 from shiltemann/mothur_datatypes 
small updates to Mothur datatypes
 2016-06-03 10:58:12 +02:00
Björn Grüning 697b01c211 Merge pull request #2438 from ThomasWollmann/dev 
fixed $defaults according to #2430
 2016-06-03 10:56:42 +02:00
John Chilton a0dbcb93a3 Merge pull request #2440 from guerler/fix_subworkflows_display 
Properly list subworkflows in run workflow form
 2016-06-02 14:41:43 -04:00
Nicola Soranzo 84ece6da37 Merge branch 'release_16.04' into dev 2016-06-02 19:38:18 +01:00
guerler 1b3eaeb299 Fix batchmode labels 2016-06-02 12:42:31 -04:00
Dannon Baker 58f3f5c7dd Merge pull request #2447 from nsoranzo/release_16.04_fix_for_2432 
[16.04] Overwrite the correct part of stderr
 2016-06-02 11:05:27 -04:00
Nicola Soranzo 7cb527ac59 Overwrite the correct part of stderr 
- Skip partial line
- Seek back to the correct position after readlines()
- Use the same approach in __check_memory_limit()
 2016-06-02 15:32:36 +01:00
Martin Cech ec476c7cb4 Merge pull request #2445 from carlfeberhard/fix.raven 
Fix raven.js import order in galaxy.panels.mako
 2016-06-02 10:24:55 -04:00
carlfeberhard f78d5404a2 Raven: remove tracekit as raven has its own 2016-06-02 09:26:16 -04:00
carlfeberhard 8ef5279aac Raven: revert previous commit and move raven first 
Moves galaxy.panels.mako's import of Raven back to vanilla script
tag and before the requirejs library import, allowing Raven's UMD
to define Raven as a global.

This starts Raven/sentry *before* the library package is loaded so that
library errors can be captured as well.
 2016-06-02 09:08:04 -04:00
carlfeberhard d458906f37 Raven: fix import in galaxy.panels.mako 
Raven now uses a UMD and checks for requirejs removing it from globals
if found. This adds a require import to load Raven.
 2016-06-02 08:51:25 -04:00
shiltemann abdae9539b update superclass accessing 2016-06-02 13:19:56 +02:00
Thomas Wollmann 1695994c84 polish 2016-06-02 09:53:19 +02:00
guerler 7eaf40ec56 Re-add new history links to success message 2016-06-01 16:27:12 -04:00
Nicola Soranzo 25a26d8c9c Merge pull request #2436 from jmchilton/galaxy_lib_testing_update 
Update Galaxy testing to target latest galaxy-lib.
 2016-06-01 15:27:57 +01:00
guerler dcd07221a8 Remove output details from success message 2016-06-01 01:21:31 -04:00
guerler 52a5f6e2db Properly display subworkflows in new run workflow form 2016-06-01 00:45:41 -04:00
Thomas Wollmann 2fc266e4ab fixed $defaults according to #2430 2016-05-31 22:47:55 +02:00
John Chilton 6da3223449 Update Galaxy testing to target latest galaxy-lib. 
Incorporates https://github.com/galaxyproject/galaxy-lib/pull/10 which modifies the interface to the test output verification code to allow reuse from within Planemo in both non-tool and non-Galaxy contexts. I also think this represents a better separation of concerns.

One upshot of this is that CWL-style checksum verification is now possible from within Galaxy tools - a test case of this is included.
 2016-05-31 14:42:10 -04:00
Dannon Baker ceb825bea8 Merge pull request #2432 from natefoo/job-output-memory-fix 
[16.04] Only scan the last 16 MB of a job's stderr for slurm memory warning messages
 2016-05-31 12:46:24 -04:00
Nate Coraor dcb28e0950 Fix linting error 2016-05-31 11:58:57 -04:00
Nate Coraor 214e757d81 Only scan the last 16 MB of a job's stderr for slurm memory warning 
messages.
 2016-05-31 11:42:36 -04:00
shiltemann 61589b378a minimize number of lines read in set_meta functions 2016-05-31 14:25:29 +02:00
Björn Grüning 835797c4ba Merge pull request #2428 from hmenager/dev 
Correct various EDAM data/format annotations in datatypes
 2016-05-30 20:39:27 +02:00
Hervé Ménager c450763e13 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev 2016-05-30 11:46:33 +02:00
Hervé Ménager 24451e75d4 add and/or correct missing EDAM formats/data to datatypes. 2016-05-30 11:43:45 +02:00
John Chilton eefc73abae Merge pull request #2416 from guerler/tool_composite_000 
Updates and fixes for the run workflow ui elements
 2016-05-28 11:17:09 -04:00
Dannon Baker 3b73bb3038 Merge pull request #2427 from martenson/minor-docs 
minor docs touch
 2016-05-27 17:07:13 -04:00
Martin Cech 3afe31649f minor docs touch 2016-05-27 15:38:48 -04:00
shiltemann b83f1b8d24 add otulabels metadata to mothur.otu datatype 2016-05-27 15:06:58 +02:00
John Chilton 6094990e43 Merge pull request #2424 from martenson/port-exceptionwrap-16.04 
[16.04] wrap bare str exceptions
 2016-05-26 18:59:43 -04:00
Dannon Baker 26ea3404ce Merge pull request #2415 from carlfeberhard/fix.show-params-hid 
Fix to 4a61a4c: add hids for dataset inputs
 2016-05-26 16:52:00 -04:00
Martin Cech fe64a8198b fix the mess made with mass edit 2016-05-26 16:45:36 -04:00
Martin Cech a27e86786a wrap bare str raises with generic Exception() 
as Pyton 2.7 does not support bare str
 2016-05-26 16:45:31 -04:00
Dannon Baker ef417464c7 Merge pull request #2421 from martenson/wrap-str-raises 
wrap bare str raises with generic Exception()
 2016-05-26 16:28:23 -04:00
Martin Cech 35da049d42 Merge pull request #2420 from nsoranzo/log_warn 
Python3: use log.warning() instead of deprecated log.warn()
 2016-05-26 14:41:21 -04:00
Martin Cech 1453dbdb13 Merge pull request #2414 from jmchilton/lib-fix 
Update galaxy-lib related modules to latest in that project.
 2016-05-26 14:22:49 -04:00
guerler 8aa629a982 Updates and fixes of the run workflow ui elements and views 2016-05-26 13:41:09 -04:00
Martin Cech 1254537075 fix the mess made with mass edit 2016-05-26 13:37:02 -04:00
Martin Cech d72eee3d4a wrap bare str raises with generic Exception() 
as Pyton 2.7 does not support bare str
 2016-05-26 13:14:22 -04:00
Nicola Soranzo 03a92abdb6 Python3: use log.warning() instead of deprecated log.warn() 
$ python3 -Wd -c 'import logging; logging.warn("foo")'
-c:1: DeprecationWarning: The 'warn' function is deprecated, use 'warning' instead
WARNING:root:foo
 2016-05-26 17:11:36 +01:00
John Chilton 4eeb73ec8c Merge pull request #2418 from nsoranzo/toolbox_watcher 
Raise Exception if watch_tools has an unrecognized value
 2016-05-26 08:17:06 -04:00
Nicola Soranzo 4bfcce0d56 Raise Exception if watch_tools has an unrecognized value 
Also do not log message "Watchdog library unavailable" if watch_tools is
False
 2016-05-26 11:59:08 +01:00