Greg Von Kuster
1e3aff12b8
Fix mercurial command line handling for pushes from the command line that were broken in change set d19fbfefb676 for versions of mercurial older than 2.2.3. Pushes should now function correctly for those running mercurial older than version 2.2.3.
2012-08-07 13:43:36 -04:00
Scott McManus
e069425ab9
Removed offending code from last checkin - sorry for the foul-up
2012-08-07 13:35:39 -04:00
Jeremy Goecks
bcc9a3b73d
Update track icons when decomposing a composite track into individual tracks.
2012-08-07 09:52:14 -04:00
Jeremy Goecks
9a5679c37c
Use mako template in tool help so that dynamic image paths can be used. Fixes #141
2012-08-07 09:40:51 -04:00
Scott McManus
92915592f9
Added minor changes, including model accessors, for cancelling PBS tasks
2012-08-05 23:45:11 -04:00
Carl Eberhard
d97ada4bb5
minor docstring adds in /scripts
2012-08-03 13:31:48 -04:00
Jeremy Goecks
29037352df
Trackster and data providers: fix and document one-off/coordinate systems used for different track types.
2012-08-03 11:20:43 -04:00
Carl Eberhard
6337e6565b
fixes for tool search clear-btn (to use templating); added bootstrap.js to tool menu iframe
2012-08-02 16:43:59 -04:00
Scott McManus
2170247eb8
Eliminated debug statements (mostly already commented out) under DELETEME tags
2012-08-02 13:06:43 -04:00
Carl Eberhard
62b0725513
btn/esc to clear tool search (bb issue #774 )
2012-08-02 12:21:49 -04:00
Scott McManus
9d6bb54e38
Fixing minor merge issue
2012-08-02 10:28:39 -04:00
Scott McManus
24328f8506
Added code to handle task deletion properly.
2012-08-01 23:27:32 -04:00
Dave Bouvier
2add218375
Reset metadata on toolshed repository when pushing a new revision with hg push
2012-08-01 14:16:07 -04:00
Greg Von Kuster
42ed06d0e6
Fixes for cloning a repository from the command line when the tool shed database is using sqlite. Also, fix for changing the name of a repository in the tool shed when the same repository is simultaneously being cloned for the first time.
2012-08-01 11:16:23 -04:00
Jeremy Goecks
72921fcad3
Trackster bug fixes: (a) fix 1-base offset bug in LineTracks; (b) fix overview track resolution calculation; and (c) code cleanup via JSHint.
2012-07-31 11:55:41 -04:00
Dannon Baker
ef9cf2b1d8
Fix tabular display to serve raw when preview == False, which should resolve external display issues.
2012-07-30 15:54:34 -04:00
Nate Coraor
0626bd36f7
Handle the varying sample ID param name ('id' or 'sample_id') in /requests_admin/manage_datasets
2012-07-27 12:39:24 -04:00
Nate Coraor
81a8350996
Document user_job_limit
2012-07-27 10:57:29 -04:00
Jeremy Goecks
f0c59b76bb
Correct size abbreviation to use uppercase B for bytes.
2012-07-27 04:08:01 -05:00
Nate Coraor
283c836654
Merged in takadonet/galaxy-central (pull request #50 )
2012-07-27 01:14:52 -05:00
Nate Coraor
8cb11c301f
Merged in JaimeFrey/galaxy-condor (pull request #51 )
2012-07-26 12:11:05 -05:00
James Taylor
a6e8a66317
tooltips: use a special even to remove tooltips automatically when their element is deleted. fix the bug deleting datasets from this history.
2012-07-25 17:08:38 -04:00
Jeremy Goecks
97ffa48a2b
Add bigwig/bigbed support to Circster. Pack scripts.
2012-07-24 14:28:08 -04:00
Jeremy Goecks
15e2cc247d
Rename paramamonster as sweepster and use bootstrap tooltips in sweepster.
2012-07-24 14:21:40 -04:00
Jeremy Goecks
134a5ad252
Trackster: only draw connector when both mates of a read are drawn; this prevents spurious connectors from being drawn but prevents connectors from being drawn across tile boundaries.
2012-07-24 14:07:06 -04:00
Remi Marenco
65da5344a0
Added eXpress sam format support + 5 parameters (-B, -O, --calc-covar, -m, -s) with their associated tests
2012-07-23 14:17:23 -04:00
James Taylor
07897fc990
style: do not define .overlay, conflicts with trackster
2012-07-23 10:38:17 -04:00
Dannon Baker
6442df74db
Merge pull request #54 from bwlang - parent tag copying for multiple workflow run output histories.
2012-07-22 18:02:43 -04:00
Dannon Baker
97c4be251d
Task runner cleanup.
2012-07-21 14:46:27 -04:00
James Taylor
2faa20f97f
style: Increase z-index of top nav tabs so the are over the brand when the window is narrow
2012-07-20 16:47:58 -04:00
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
Greg Von Kuster