Kanwei Li
5cf8668d64
trackster: don't show tile if no tile (fixes ReferenceTrack)
2011-04-19 14:20:11 -04:00
Daniel Blankenberg
ee5400e2ad
Add missing test file from 5407:b387de5c0439.
2011-04-19 11:49:18 -04:00
Greg Von Kuster
938f4f490c
Improved exception handling in the tool shed.
2011-04-19 10:20:01 -04:00
James Taylor
cf89619aca
trackster: for line painter, determine min and max from data if not provided (not actually used for trackster)
2011-04-19 09:44:28 -04:00
Nate Coraor
33ad7a4984
Add enable_tool_tags to the sample configuration file.
2011-04-19 08:24:57 -04:00
Nate Coraor
7535161d6d
Make all tool tag related functionality conditional on 'enable_tool_tags = True' in the Galaxy configuration file.
2011-04-19 08:22:48 -04:00
Nate Coraor
467885c59d
Merge changes from the NBIC Galaxy Hackathon. Includes the addition of scripts which automatically generate the tool_conf.xml from tool configuration files. Tool configuration files also support optional syntax which specifies their placement in sections, as well as what tags the tool should be associated with. Also includes support for associating tags with tool IDs and filtering tools by tag in the tool menu.
2011-04-19 08:21:54 -04:00
Kanwei Li
c9c279ae6c
New pysam for solaris fixes
2011-04-19 00:07:36 -04:00
Kanwei Li
b2ba5d422a
trackster:
...
- Use tabix (through pysam) as the indexer for feature formats. Bed support included in this commit
- Add bigBed format support (same interface as bigWig)
- Improve implicit converter error handling
2011-04-18 18:07:52 -04:00
Kanwei Li
6802b93c7c
trackster: Small UI tweaks
2011-04-18 17:02:32 -04:00
Nate Coraor
5ec375f673
merge
2011-04-18 16:43:35 -04:00
Nate Coraor
ec59ea0b30
Update bx-python to the tip.
2011-04-18 16:42:12 -04:00
Daniel Blankenberg
22e3e53ce0
Enhance BAM to SAM tool to optionally output headers.
2011-04-18 16:41:51 -04:00
Nate Coraor
13b42fde9a
Just build on Solaris 10 for sparc. Apologies to anyone running a 9+ year old OS. ;)
2011-04-18 16:41:38 -04:00
Nate Coraor
f60a292e91
Scramble script for bx-python on Solaris (needs some C99 defines).
2011-04-18 16:40:43 -04:00
Kanwei Li
51acb08b30
trackster: Fix page switch links breaking in Add Tracks menu, restore Last Updated column
2011-04-18 14:35:14 -04:00
Nate Coraor
96ef29d991
Use Egg.fetch() instead of Egg.resolve() to get dependencies when dist-scrambling.
2011-04-18 14:04:06 -04:00
Greg Von Kuster
5fa67fa134
Fixes for external service file browser.
2011-04-15 16:37:56 -04:00
Daniel Blankenberg
4bb2ac729b
Update help and description for Draw ROC plot tool. Questions and comments should be directed to Chungoo Park.
2011-04-15 13:55:45 -04:00
Jeremy Goecks
4b636226b9
Trackster visual analytics: set initial parameter values properly.
2011-04-15 09:42:55 -04:00
Ross Lazarus
50e1bb9f4c
title not alt for popups on thumbnails for Haploview outputs
2011-04-15 09:35:41 -04:00
Dannon Baker
4512e0df4f
Workflow Parameter bugfix for the case when a parameter isn't used in
...
any workflow step, but should still be available for PJAs.
2011-04-14 23:40:19 -04:00
Kanwei Li
4797b23824
trackster:
...
- UI support for adding datasets from Data Libraries
- Cleaner, more consistent "Add Tracks" dialog that implements above
Sync .css changes with their corresponding .css.tmpl template
2011-04-14 20:25:54 -04:00
James Taylor
afd540aef7
Automated merge with https://bitbucket.org/galaxy/galaxy-central
2011-04-14 16:51:40 -04:00
James Taylor
7a7572648b
trackster: fix problem with drawing bounderies of overflow bars for line tracks
2011-04-14 16:51:26 -04:00
Greg Von Kuster
0d1f540e99
Fixes for transferring files from external services using the http protocol. Automatic file transfers from Pac Bio SMRT Portal are functional for version 1.1.0.
2011-04-14 16:42:12 -04:00
Jeremy Goecks
f514b9471e
Create and use ReferenceTrackDataManager to fetch ReferenceTrack data.
2011-04-14 14:34:39 -04:00
James Taylor
1c0267840c
Automated merge with https://bitbucket.org/galaxy/galaxy-central
2011-04-14 14:32:44 -04:00
James Taylor
b644ad2506
merging
2011-04-14 14:32:37 -04:00
Jeremy Goecks
23efa70ebe
Trackster: (a) fix bug in acee660871cd that prevented line tracks from displaying properly and (b) set track height in show_tile rather than draw_tile, which obviates the need for parent_element to be passed to draw_tile.
2011-04-14 14:29:32 -04:00
James Taylor
ecfa51199f
Automated merge with https://bitbucket.org/galaxy/galaxy-central
2011-04-14 14:07:22 -04:00
Jeremy Goecks
254018a930
Trackster: refactor so that summary_tree and Histogram modes use the same code.
2011-04-14 10:37:42 -04:00
Jeremy Goecks
ffc478709b
Fix bug that prevented workflows with runtime parameters from being exported.
2011-04-14 10:05:00 -04:00
vdtoorn@hotmail.com
1c221447e9
introduction of toolboxposition elements
2011-04-14 15:09:00 +02:00
Dannon Baker
859d15f7cc
Merge!
2011-04-14 09:02:20 -04:00
Martijn Vermaat
9964bd8673
Give input selection and filtering a minimum width (run tool form).
2011-04-14 14:23:28 +02:00
Nate Coraor
1202b6e3d0
Fix the spinner in the tool search box when tags are enabled.
2011-04-14 14:23:15 +02:00
Freek de Bruijn
b237a87ef2
Alex and Freek: clear the tool tag associations in init_tools before adding these associations.
2011-04-14 14:20:48 +02:00
Rob Hooft
020597d197
* merge
2011-04-14 14:09:54 +02:00
Ross Lazarus
ee6bd2cf46
Changes to allow all test outputs generated by twill to be saved to a folder pointed to by
...
an environment variable "GALAXY_TEST_SAVE" if defined before running functional tests
If the environment variable is empty, all tests procede as usual and test outputs are deleted
without saving
2011-04-14 08:09:48 -04:00
Rob Hooft
db3fae4c2b
* Remove Todo's that have been done
2011-04-14 14:07:36 +02:00
Rob Hooft
f04e5682b4
* Restructured to use toolboxposition elements instead of section elements. Now
...
handles order and labels
2011-04-14 14:07:05 +02:00
Nate Coraor
777043352e
Persist tool tag selections for logged-in users.
2011-04-14 13:54:46 +02:00
Nate Coraor
c12968d7da
Fix for searching tools, and then selecting tags. Also refactoring to remove duplicated javascript.
2011-04-14 12:44:25 +02:00
Martijn Vermaat
71e298cdcb
Adds filtering to input selection on run workflow page.
2011-04-14 12:14:30 +02:00
Nate Coraor
4515f0b8cd
More functionality for tool tags, still needs to be refactored to remove javascript duplicated from the tool search.
2011-04-14 10:53:22 +02:00
Rob Hooft
e8c98020d6
* Special cased the "off" tag to leave a tool out of the toolbox.
2011-04-14 10:02:10 +02:00
Dannon Baker
2c81457e57
Merge.
2011-04-13 19:14:21 -04:00
Martijn Vermaat
100db97731
Typo.
2011-04-14 01:13:10 +02:00
Dannon Baker
254876a817
Merge.
2011-04-13 19:07:22 -04:00
Kanwei Li