Nicola Soranzo
46641daaa7
Merge galaxy/galaxy-central default branch.
2014-04-11 12:00:39 +02:00
Jeremy Goecks
80b603902a
Merge next-stable branch to default.
2014-04-10 17:21:38 -04:00
Jeremy Goecks
28ddf4bcc2
Updates to Sweepster to get it working again.
2014-04-10 17:21:00 -04:00
Greg Von Kuster
8bce650dda
Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.
2014-04-10 17:11:01 -04:00
Daniel Blankenberg
34f9066503
merge next-stable
2014-04-10 16:48:31 -04:00
Daniel Blankenberg
c5f3f75ad5
Fix for route used in displaying images on tool installed from a toolshed.
2014-04-10 16:48:07 -04:00
Martin Cech
6854dbd523
history API: allow anon users import public datasets into their (only) history, add exception for unknown datatype
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library API: don't show folders without single accesible item to anonyms
2014-04-10 16:45:59 -04:00
Carl Eberhard
8f179efe71
Metrics: initial commit of client side logger
2014-04-10 16:28:16 -04:00
Daniel Blankenberg
c3a29f9fb6
Add a link to a tool's toolshed repository if it was installed from a ToolShed.
2014-04-10 15:55:26 -04:00
Martin Cech
4bea6249f3
forgotten files for previous commit
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data libraries: API refactoring and improvements; backbone decoupling; role UI first implementation
2014-04-10 15:07:01 -04:00
Martin Cech
0dd3187401
data libraries: API refactoring and improvements; backbone decoupling; role UI first implementation
2014-04-10 15:05:33 -04:00
John Chilton
86ee4fdabf
Simplify enable_output_terminal and enable_output_terminal in workflow editor.
...
These functions were taking in a single element and then looping through it. I hope this is not some intententional jQuery pattern to change the value of 'this' I don't quite understand and is just a remnant of when some loop over inputs was on the inside of this function or some other such refactoring.
2014-04-10 13:31:48 -05:00
John Chilton
7b2c20cc46
Outline workflow editor tests.
2014-04-10 13:31:48 -05:00
John Chilton
69ddb38557
Refactor interaction between workflows JS and editor JS for adding nodes.
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Add abstraction into editor for use by galaxy.workflow.js to hide some editor details from workflow code and reduce duplication between add_node_for_tool and add_node_for_module.
2014-04-10 13:31:47 -05:00
John Chilton
9b0bbb0dab
Remove unused variable?
2014-04-10 13:31:46 -05:00
Dave Bouvier
b00928c1be
Merge with next-stable.
2014-04-10 14:01:59 -04:00
Nicola Soranzo
f73d5fba6c
Fix old wiki links.
2014-04-10 20:00:45 +02:00
Dave Bouvier
7da3f0a6aa
Corrected version for migrated tools.
2014-04-10 13:59:40 -04:00
Nicola Soranzo
61c427c154
Fix a broken import. Cleanup imports.
2014-04-10 19:57:25 +02:00
Nicola Soranzo
d7b542d3c2
PEP8 whitespace fixes.
2014-04-10 19:56:43 +02:00
Daniel Blankenberg
2b52d39816
Change suc.get_url_from_tool_shed to common_util.get_tool_shed_url_from_tool_shed_registry.
2014-04-10 13:49:43 -04:00
Daniel Blankenberg
ed52fb0cd2
merge next-stable
2014-04-10 13:40:00 -04:00
Daniel Blankenberg
e83208a0c1
When posting to BioStar include a ToolShed url, as applicable.
2014-04-10 13:39:41 -04:00
Daniel Blankenberg
d197d2c17b
Include tool version information in bug reports.
2014-04-10 13:38:44 -04:00
Nicola Soranzo
54da17c1ef
Remove unused method. Cleanup imports.
2014-04-10 18:35:18 +02:00
Nicola Soranzo
02dae93ad0
Remove unused method.
2014-04-10 18:22:32 +02:00
Greg Von Kuster
b436a8082f
Display repository dependency definition attributes for repositories being installed into Galaxy where the dependency hierarchy cannot be determined likely due to invalid dependency definitions.
2014-04-10 11:35:37 -04:00
Aysam Guerler
273c962f0d
Charts: Add label selection columns
2014-04-10 10:00:54 -04:00
John Chilton
9c1bf4c740
Thanks Trevor!
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Merged in trevorw/galaxy-central-5/trevorw/job_directory-jobs_directory-1397077266550 (pull request #360 )
job_directory -> jobs_directory
2014-04-10 08:51:47 -05:00
Greg Von Kuster
9c29c424d9
Fix in the tool shed install and test framework for a recently relocated function.
2014-04-10 07:20:27 -04:00
Aysam Guerler
3132c5e1e6
Charts: Allow switching chart types without reset, fix resizing
2014-04-09 20:50:45 -04:00
Daniel Blankenberg
4d88ce03de
Improve handling of invalid/expired GenomeSpace tokens in GenomeSpace export tool.
2014-04-09 17:24:56 -04:00
Trevor Wennblom
5616b289cb
job_directory -> jobs_directory
2014-04-09 21:02:33 +00:00
Carl Eberhard
86da018f62
Metrics API: allow posting of metrics sending to app.trace_logger.log if available
2014-04-09 16:15:00 -04:00
Jeremy Goecks
be37a0846c
Automated merge of next-stable to default.
2014-04-09 12:53:57 -04:00
Jeremy Goecks
38452da57a
SAM/BAM data provider: fix bug and streamline code to support both genomes with reference data and those without.
2014-04-09 12:53:34 -04:00
Jeremy Goecks
c892a67f13
Genome data provider: (a) handle regions with no mapped reads and (b) clean up trailing whitespace.
2014-04-09 10:47:22 -04:00
Greg Von Kuster
27e60943bf
The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.
2014-04-09 10:11:48 -04:00
Daniel Blankenberg
dc6aba0497
merge next-stable
2014-04-08 17:05:21 -04:00
Daniel Blankenberg
6c704a4e7f
fix tab spaces in javascript
2014-04-08 17:05:09 -04:00
Daniel Blankenberg
d9a8d92695
merge next-stable
2014-04-08 17:03:38 -04:00
Daniel Blankenberg
cee2ac4485
When submiting bug reports disable submit buttons while form is being submitted. When submiting bug report to Biostar, have user confirm that they are posting to a public forum.
2014-04-08 17:03:19 -04:00
Carl Eberhard
8207cb0043
merge next-stable
2014-04-08 14:14:58 -04:00
Carl Eberhard
d7dda26c58
Remove debugging statements
2014-04-08 14:14:17 -04:00
Carl Eberhard
5120673dbd
Metrics: allow time to be passed into fluent_log.py, log
2014-04-08 12:55:30 -04:00
Jeremy Goecks
6366ef405e
Automated merge of next-stable to default
2014-04-08 12:08:20 -04:00
Jeremy Goecks
9d64557de5
Trackster: update jQuery selector so that all tool inputs are updated on change rather only <input> elements. Pack script.
2014-04-08 12:07:50 -04:00
Aysam Guerler
09d1f2811f
Charts: Add libraries
2014-04-07 19:19:42 -04:00
Aysam Guerler
fb48f9889f
Charts: Add boxplots
2014-04-07 19:18:25 -04:00
hillrunner2008
148dcc474c
Merged galaxy/galaxy-central into default
2014-04-07 16:31:01 -04:00
Nicola Soranzo