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807 Commits
Author SHA1 Message Date
Remi Marenco c8469b7d0e Refactor the Html Datatype Class into text.py instead of images.py 2016-02-18 13:01:07 -05:00
Nicola Soranzo 2ddf6eed63 Remove broken and hidden fix_errors tool. 2016-02-10 17:35:25 +00:00
John Chilton eab2f1ff5c Merge pull request #1665 from lecorguille/zip_datatype 
add a zip datatype which won't be extracted
 2016-02-08 13:43:49 -05:00
Saskia Hiltemann 674bf530c6 fix window height issue 2016-02-05 10:51:47 +01:00
Saskia Hiltemann 1b04ba3833 use bioblend for dataset import instead of mount 2016-02-04 11:02:11 +01:00
John Chilton e106609c1c Add a more correct zip file type. 2016-02-03 13:33:04 +00:00
Gildas Le Corguillé 87f3ee48b0 add a zip datatype which won't be extracted 2016-02-03 16:46:50 +01:00
shiltemann 87b5ba458f changed docker tag to fit with Galaxy release 2016-02-03 10:41:55 +01:00
shiltemann ebb41225be added Phinch interactive environment 2016-02-02 11:08:31 +01:00
Nate Coraor 28c4b49e8d Various improvements to the heartbeat: 
- Dump on `SIGUSR1`
- Configurable dump period (including "no periodic dump, signal only")
- Default log filename now includes server_name so logs do not clobber
  eachother
- Configurable/templateable log filename
- Catch more sleeping threads
- Use write() instead of print
 2016-01-28 13:50:45 -05:00
John Chilton b77b096a38 Merge pull request #1582 from matthdsm/patch-1 
small spelling error
 2016-01-26 09:11:29 -05:00
matthdsm 29734512ab small spelling error 
maxiumum > maximum
 2016-01-26 14:58:48 +01:00
John Chilton 807586ace8 Merge release_16.01 into dev. 2016-01-26 09:06:52 +00:00
carlfeberhard bf459c8d55 UI: (cleaning up) remove handlebars compiled/map and remaining references 2016-01-19 14:12:28 -05:00
carlfeberhard 4ea5f15edd Scatterplot: remove handlebars by converting to underscore, remove grunt handlebars task 2016-01-19 13:57:49 -05:00
carlfeberhard 49a72dacc6 Merge pull request #1519 from guerler/refactor_000 
Cleanup common ui elements, add test cases
 2016-01-15 10:49:35 -05:00
John Chilton 274af50792 Merge pull request #1331 from carlfeberhard/CORS 
Core, CORS: allow (non-preflighted) CORS requests by echoing back the…
 2016-01-15 10:44:50 -05:00
guerler 03082a7239 Fix test label 2016-01-14 18:52:08 -05:00
guerler b38bc293d7 Add Scratchbook tour 2016-01-14 09:02:29 -05:00
John Chilton 793fbdbedc Merge remote-tracking branch 'jmchilton/release_16.01' into dev_merge_0 
Conflicts:
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
 2016-01-14 07:44:48 +00:00
John Chilton 602dc7f664 Switch default job shell back to /bin/sh for 16.01. 2016-01-14 06:17:45 +00:00
John Chilton 3e47aa23b8 Switch to bash as default shell (for conda resolver). 
I'm making more things configurable in case someday the BSD user wants to use Galaxy - the default shell for jobs can be configured at the galaxy or job destination level now.
 2016-01-14 06:17:43 +00:00
John Chilton 55677f2d3d Fix to ensure integrity of tool_script.sh also. 
Previously the job script underwent these checks and I had assumed since that got written later it would never be the case that tool_script.sh wouldn't be synchronized by the job script was - turns out file systems are more creative and less logical than one might expected.

Also increases the count for the number of syncs that will execute because 15 on rare occasion proved not to be enough as well as making both the count and sleep time configurable.
 2016-01-13 14:58:28 +00:00
John Chilton ea5c082e88 Merge pull request #1402 from bgruening/remove_ipython 
Remove IPython IE, which was replaced by Jupyter IE.
 2016-01-12 18:53:07 -05:00
Dannon Baker f939c4eab5 Merge from release to dev. 2016-01-12 14:58:57 -05:00
Björn Grüning d2702e9e44 Fix spelling mistake spotted by Nicola 2016-01-11 16:17:09 +01:00
Bjoern Gruening 252586f86c improve default tours 2016-01-10 23:26:55 +01:00
Björn Grüning 016fd38e72 Merge pull request #1148 from markiskander/bcfgz_to_bcf_converter 
Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type
 2016-01-06 11:48:33 +01:00
carlfeberhard 80cce3f428 CORS: remove basestring, remove log, null-proofing, allow unicode regexp, add testing 2016-01-05 14:28:47 -05:00
Dannon Baker 3d1b3f9806 How'd that get there? 2016-01-05 13:23:03 -05:00
carlfeberhard d717f26581 Merge remote-tracking branch 'upstream/dev' into CORS 2016-01-05 10:40:02 -05:00
John Chilton 7587809bb6 Improve tour directory logic. 
- Refactor plugin framework logic for finding configuration directories out into util.
 - Rework tours to use the plugin framework logic to parse configuration directories.
 - Rework tour logic to allow multiple tour configuration directories.
 - Fix up config.ini.sample comments on interactive environments and tours to reflect these changes and include more information like the viz directory does.
 2016-01-05 00:28:24 +00:00
Dannon Baker c28d4d01ee Correctly specify default tour location. 2016-01-04 22:39:56 -05:00
Dannon Baker da8b943f53 Merge. 2016-01-04 19:23:06 -05:00
Dannon Baker d235410920 Remove tour id from tour; unique and namespaced by filename and not a separate identifier. 2016-01-04 17:13:19 -05:00
Dannon Baker 603cb2f18d Add history tour from @bgruening 2016-01-04 09:52:47 -05:00
Björn Grüning 34bb21c411 Merge pull request #1407 from guerler/revise_masthead_000 
Masthead/Scratchbook revision and test cases
 2016-01-04 01:31:44 +01:00
Björn Grüning 905adbac38 Merge pull request #1412 from jmchilton/isolate 
Isolate tool commands by default.
 2016-01-04 01:28:41 +01:00
John Chilton 4086dd61da Implement toolbox monitoring. 
- Add monitor tag on toolbox root elements to force Galaxy to watch the toolbox for changes.
 - Refactoring and test improvements for existing tool monitoring code.
 - Implement toolbox shutdown process to ensure different watchers don't compete with each other.
 - Set the default tool conf to be monitored.
 2016-01-03 13:10:08 +00:00
John Chilton a6cbb88ad1 Enable tool isolation by default and fix bugs. 2016-01-02 14:17:08 +00:00
guerler 339ad57f3f Cleanup Masthead and Scratchbook 
Cleanup Masthead and Scratchbook
 2015-12-30 16:31:59 -05:00
Eric Rasche 0aa1c5133e Merge pull request #1345 from jmchilton/conda_0 
Implement a conda dependency resolver.
 2015-12-30 15:03:52 -06:00
Dannon Baker 4322f5e9b9 Force tour_id to be locked to filename, instead of allowing these to be out of sync. 2015-12-29 09:26:18 -05:00
Bjoern Gruening a26c975964 Remove IPython IE, which was replaced by Jupyter IE. 2015-12-27 21:37:52 +01:00
Bjoern Gruening 6ac01675f3 Change default image name to a versioned tagged Docker release. 2015-12-27 01:49:38 +01:00
Bjoern Gruening 38d40e7af1 move keep_alive into jupyter.js 2015-12-27 01:46:50 +01:00
John Chilton 1148081435 Implement a conda dependency resolver. 
Much more information on planemo PR that I used to build a test bed for this:

https://github.com/galaxyproject/planemo/pull/392

Also syncs galaxy with planemo shared library changed.
 2015-12-26 22:46:28 +00:00
Bjoern Gruening 47a4420267 Add Jupyter Interactive Environment 2015-12-25 22:59:32 +01:00
Dannon Baker e325eba37c Some tweaks care of @bgruening. This adds (slightly tweaked) functionality to support a series of clicks, still needs a delay between clicks, and since it's the most common case that pre/postclick will be a single item, a list shouldn't be required here. 2015-12-21 13:08:15 -05:00
Dannon Baker aecc5d864f Make tours.js safe (but possibly not functional wrt/ listing) to use on pages without Galaxy object. 2015-12-18 16:24:19 -05:00