James Taylor
901b042c0b
Add bootstrap transition to bootstrap.js, makes animations much more tolerable
2012-07-20 16:43:13 -04:00
James Taylor
3118446f4e
tooltips: Replace all uses of tipsy with bootstrap style (with the same modifications for placement we previously used for tipsy). This will allow us to start using popovers
2012-07-20 16:28:23 -04:00
Brad Langhorst
331d218056
copies the tags from a source history when a workflow is creating new histories to store results.
...
moves tag copying logic into the model for TagAssociation class
adds copy_tags_from method to history and storedworkflow classes
2012-07-20 15:15:14 -04:00
James Taylor
96f6ea514b
Add support for bootstrap style tabs, use tabs in edit attributes form
2012-07-20 14:53:30 -04:00
James Taylor
83b5e65622
styles: We are not using icons from bootstrap so don't build in the sprites
2012-07-20 14:15:45 -04:00
James Taylor
b2d9d0223c
Automated merge with https://bitbucket.org/galaxy/galaxy-central
2012-07-20 14:08:53 -04:00
James Taylor
43d6d27fe8
styles: Removed old styles (old_blue_style and light_hatched_style) that can't possibly work anymore
2012-07-20 14:08:36 -04:00
James Taylor
b83987b290
styles: Update to bootstrap 2.0.4. The bootstrap directory is now an *exact*
...
clone from github. Variables have been moved to
"galaxy_bootstrap_variables.less" for easy synchronization with upstream
variable additions. Changes that couldn't be made through variables are now
overrides in "galaxy_bootstrap.less" or "base.less"
2012-07-20 14:02:07 -04:00
Jeremy Goecks
0c00e50a54
Move implementation of from_work_dir attribute from job finish to job command line so that outputs are available earlier. This provides compatibility of attribute when setting metadata externally. Update Tophat wrapper to act as exemplar for attribute use.
2012-07-20 13:18:54 -04:00
James Taylor
f66e05e00a
remove reference to modernizr in base_panels, not yet used
2012-07-20 11:26:17 -04:00
James Taylor
25325e9208
Automated merge with https://bitbucket.org/galaxy/galaxy-central
2012-07-19 13:56:48 -04:00
James Taylor
bfbea0e199
Add a message to the root index page for browsers without javascript.
2012-07-19 13:55:48 -04:00
Jeremy Goecks
6a591eb48b
Viz framework: bigwig fixes and remove unnecessary type casting.
2012-07-19 10:59:20 -04:00
Jeremy Goecks
5756d21059
Do not use route memory for dataset save URLs because it introduces harmful parameters.
2012-07-19 09:45:48 -04:00
James Taylor
ccfc8ce3a7
Automated merge with https://bitbucket.org/galaxy/galaxy-central
2012-07-18 18:22:52 -04:00
Jeremy Goecks
9b2ec24928
Reintroduce directionality indication to single-block features as it is again compatible with current code.
2012-07-18 17:52:54 -04:00
Jeremy Goecks
adfb80b77e
Encode dataset id for dataset returned when rerunning tools.
2012-07-18 15:50:37 -04:00
Jeremy Goecks
be3f87204c
Code cleanup using JSHint.
2012-07-18 15:46:26 -04:00
Remi Marenco
44701c866d
Merge
...
Hg: changed lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py
2012-07-18 10:48:59 -04:00
Remi Marenco
dd7f9dc3a7
eXpress tool wrapped in Galaxy. Added in "NGS: RNA Analysis".
2012-07-17 17:12:51 -04:00
Jeremy Goecks
13e2de0f01
Scope a1276b504934 to tool form inputs only.
2012-07-16 21:10:39 -04:00
Jeremy Goecks
55d0b2b751
Fix Trackster bug that was erroneously fetching reference data. Pack script.
2012-07-15 19:18:26 -04:00
Jeremy Goecks
b52909ad4a
Add icon to get from Trackster to Circster.
2012-07-15 19:02:59 -04:00
Jeremy Goecks
ef753ff3f2
Trackster: make sliders more responsive by waiting before drawing.
2012-07-13 19:44:21 -04:00
Greg Von Kuster
5232d4e52c
Make sure a shed related tool config is defined in universe_wsgi.ini before allowing automatic tool installs from a tool shed.
2012-07-13 19:09:51 -04:00
Jeremy Goecks
e38c49ea15
Tracks: make composite tracks compatible with recent Backbone enhancements and (b) whitespace cleanup.
2012-07-13 17:55:29 -04:00
Dave Bouvier
b58678c534
Show an error message during tool installation if tool_dependency_dir is unset.
2012-07-13 14:18:15 -04:00
Dave Bouvier
e6cf2f421b
Set tool dependency status to installed if the dependency is already installed.
2012-07-13 13:31:12 -04:00
Greg Von Kuster
7992dfa449
Another change to installed changed revision for the freebayes tool migration process.
2012-07-13 12:53:42 -04:00
Greg Von Kuster
2c87a63983
Change ethe installed changed revision for the freebayes tool migration process.
2012-07-13 12:50:29 -04:00
Greg Von Kuster
e1a5acd283
Revert my last change set.
2012-07-13 12:37:45 -04:00
Greg Von Kuster
117d077303
Pritorize tools first, followed by proprietary datatypes and then workflows when setting metadata on tool shed repositories.
2012-07-13 12:12:08 -04:00
Greg Von Kuster
56506808be
Fix for transferring datasets in sample tracking.
2012-07-13 10:15:49 -04:00
Jeremy Goecks
40a85af02f
Use same colors for all tracks in parameter space viz.
2012-07-12 19:05:48 -04:00
Jeremy Goecks
94927ee10a
Pack script.
2012-07-12 15:53:32 -04:00
Jeremy Goecks
2176031471
Fix Trackster bug.
2012-07-12 15:53:00 -04:00
Nate Coraor
2fc9c6312e
Add links to terms and conditions.
2012-07-12 14:05:55 -04:00
Jeremy Goecks
efc17f5f5f
Render all tracks in Circster using track preferences.
2012-07-12 13:21:16 -04:00
Jeremy Goecks
1bc8dd1b6b
SummaryTree improvements: (a) establish and use attribute defaults; (b) use dynamic cutoffs for detail/draw rather than static ones.
2012-07-12 11:08:08 -04:00
Jeremy Goecks
f0540824e1
Fix style of search submission icon in grids to prevent wrapping.
2012-07-12 09:43:21 -04:00
Jeremy Goecks
59dbff3de7
Bring grid button styles into alignment.
2012-07-12 08:59:34 -04:00
Dannon Baker
7f16e59a0c
Fix issue caused in 1827729ed37e that failed to correctly order task directories prior to merging, and, whitespace cleanup.
2012-07-11 16:53:59 -07:00
Greg Von Kuster
c98d5eb7b1
Fixes for installing / reinstalling tool shed repositories.
2012-07-11 17:32:27 -04:00
Greg Von Kuster
bd4bd31f6d
Don't reset the status on installed tool dependencies when getting updates from the tool shed for installed tool shed repositories.
2012-07-11 13:45:42 -04:00
Jeremy Goecks
aa4f9ae4e2
Small viz tweaks.
2012-07-11 13:19:23 -04:00
Daniel Blankenberg
47ab6aefc6
Fix for history items going to different histories if current history is switched while the workflow is still being queued.
2012-07-11 12:01:16 -04:00
Greg Von Kuster
5bac638848
Fixes for installing tool dependencies, and uninstalling repositories and tool dependencies.
2012-07-11 11:53:22 -04:00
Greg Von Kuster
7d95fcd013
Fix the sqlite db connection string in the community app so local tool sheds will work when using sqlite.
2012-07-11 10:47:51 -04:00
Daniel Blankenberg
b2c152dbf8
Remove FreeBayes from tool_conf.xml.sample/main since it has been migrated to the toolshed.
2012-07-10 17:35:30 -04:00
Remi Marenco
a7ef6336ac
Automerge
2012-07-10 17:23:56 -04:00
James Taylor