Jeremy Goecks
d2d7358d2e
Make trackster View object into a Backbone view.
2012-10-22 12:33:30 -04:00
Jeremy Goecks
f5c66342f1
Enable Tophat, Tophat2, and Cuffdiff to accept gene annotations in GFF3 format. Thanks to Jim Johnson.
2012-10-22 10:52:48 -04:00
Jeremy Goecks
069092f96b
Code cleanup in vis framework.
2012-10-22 10:47:46 -04:00
Greg Von Kuster
c702cc0fe5
Apply patches from John Chilton to resolve the issues where (1) Galaxy doesn't load tool sections from multiple files in a consistent manner, and (2) John's standing request in the now-defunct Galaxy bitbucket bug tracker to allow directories to appear in the tool_config_file option.
2012-10-22 10:43:59 -04:00
Jeremy Goecks
2607d1b3c0
Pack scripts.
2012-10-20 16:40:38 -04:00
Jeremy Goecks
19d968863c
Circster, cleanup for fetching more data: do not fetch more data for summary tree and use linear function for fetching more bigwig data.
2012-10-20 16:39:39 -04:00
Jeremy Goecks
fc7000b8bf
Circster: code cleanup to remove use of options dictionary.
2012-10-20 16:25:28 -04:00
Jeremy Goecks
4161d08f04
Circster: transition paths when loading more detailed data.
2012-10-20 16:12:00 -04:00
Jeremy Goecks
83d080f451
Better data handling when downloading history export files.
2012-10-20 14:40:42 -04:00
Jeremy Goecks
636e398345
Make Trackster use generic visualization save functionality.
2012-10-20 13:16:22 -04:00
Jeremy Goecks
6e5653bdff
merge
2012-10-19 21:08:16 -04:00
Jeremy Goecks
fefa6ac501
Circster: add programmatic support for removing tracks.
2012-10-19 21:07:56 -04:00
Nate Coraor
53426bcd1e
merge zero-merge to default.
2012-10-19 16:28:19 -04:00
Nate Coraor
c37e445600
Closed branch zero-merge.
2012-10-19 16:27:48 -04:00
Greg Von Kuster
fe8d5766df
Some tool she drepository grid cleanup, and add the ability to mark a repository as deprecated / undeprecated. Repositories in the tool shed that are marked as deprecated have restricted tool shed features and will not be included in several queries.
2012-10-19 16:25:08 -04:00
Scott McManus
e567248038
Merged in peterjc/galaxy-central/zero-merge (pull request #78 )
2012-10-19 15:53:49 -04:00
Daniel Blankenberg
a986bcde0e
Minor enhancements for GenomeSpace import naming of secondary files.
2012-10-19 15:26:51 -04:00
Jeremy Goecks
64670ceb98
Set up track config in BackboneTrack objects and use config in Circster.
2012-10-19 14:02:23 -04:00
Nate Coraor
78ffff3795
Retry pbs_submit if it fails.
2012-10-19 12:56:10 -04:00
Jeremy Goecks
9c953192be
Add backbone model, collection, and view for configuration settings. Pack scripts.
2012-10-19 11:55:49 -04:00
Peter Cock
b7d245fee7
Log nothing to merge to stderr
2012-10-19 15:23:02 +01:00
Peter Cock
b1de0a83b6
Don't attempt to merge zero files
2012-10-19 14:51:37 +01:00
Peter Cock
7bfe77fe03
Error when attempt to merge zero files.
...
Previously the code would try to call cat with no arguments,
which would wait for stdin and so do nothing and stall.
This error condition could be triggered with a cluster job
when Galaxy didn't get any output back.
2012-10-19 14:02:54 +01:00
Greg Von Kuster
719cf7d582
Pass ids instead of objects when managing reviews from certain tool shed locations.
2012-10-18 16:51:36 -04:00
Greg Von Kuster
aaf011b269
fix typo.
2012-10-18 16:35:06 -04:00
Greg Von Kuster
adfedac208
Be able to find the desired review when choosing to manage it from various places in the tool shed.
2012-10-18 16:32:33 -04:00
Greg Von Kuster
3c57eeec57
Add the ability to search for repositories in the new review grids.
2012-10-18 16:14:35 -04:00
Greg Von Kuster
ba31fcea6c
Add the ability to review a defined (but flexible) set of repository components for repositories in the tool shed. Reviews are performed on specific revisions of the repository that are installable at the time of review. Each repository component can be reviewed and approved (or not) as well as rated. The repository revision is automatically rated as the average of all component ratings. The repository revision can be approved (or not) in addition to each component. Component reviews can be marked "private", in which case they are only accessible by the owner and the group of reviewers. The ability to review repositories is restricted by the tool shed's role-base access security components. Initially, all member of the Intergalactic Utilities Commission can review repositories.
2012-10-18 15:47:06 -04:00
Daniel Blankenberg
b9decbc7cf
Do not hide failed datasets with HideDatasetAction post job action.
2012-10-18 11:22:12 -04:00
Daniel Blankenberg
bc676989d8
Unhide failed output datasets.
2012-10-18 11:22:12 -04:00
Scott McManus
811dcc9a5c
Fixed minor issue with folder API's routing.
2012-10-17 22:55:00 -04:00
Scott McManus
e546fd3add
Minor cleanup
2012-10-17 18:01:45 -04:00
Scott McManus
fa40ddd742
Removed experimental code for improving library browsing performance
2012-10-17 17:40:25 -04:00
Daniel Blankenberg
6558a52683
Fix importing ordering of boto in cloudlaunch.
2012-10-17 16:14:17 -04:00
Daniel Blankenberg
6f7b8190b8
Fix for enumerator in python2.5 in datatype sniffer
2012-10-17 16:06:22 -04:00
Daniel Blankenberg
0e79d158b0
Use simplejson for python2.5 compatibility in genome index.
2012-10-17 16:06:20 -04:00
Daniel Blankenberg
d9a4e8e229
Fix for trying to set httponly cookie attribute for python2.5 compatibility.
2012-10-17 15:56:29 -04:00
Daniel Blankenberg
f665c137c8
Use simplejson in data_admin for python2.5 compatibility.
2012-10-17 15:56:12 -04:00
Daniel Blankenberg
3d714f2d47
Use simplejson in lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py for python2.5 compatibility.
2012-10-17 15:56:12 -04:00
Daniel Blankenberg
2bea8238e9
Use simplejson in lib/galaxy/visualization/data_providers/phyloviz/newickparser.py for python2.5 compatibility.
2012-10-17 15:56:12 -04:00
Daniel Blankenberg
e7afa45382
Use simplejson in lib/galaxy/visualization/data_providers/phyloviz/baseparser.py for python2.5 compatibility.
2012-10-17 15:56:12 -04:00
Daniel Blankenberg
c714bef8f4
Fix file read sentinel. Use simplejson for python2.5 compatibility in genome index.
2012-10-17 15:56:12 -04:00
Daniel Blankenberg
0801f0c0b4
Have exit range isinf test use util.isinf for python2.5 compatibility.
2012-10-17 15:56:11 -04:00
Daniel Blankenberg
517d5739b8
Add util.isinf function.
2012-10-17 15:56:11 -04:00
Dannon Baker
a95bd1e01a
CloudLaunch: Add password confirm field to cloudlaunch to prevent accidentally not knowing your password during presentations.
...
Actually display errormessage box to show issues.
2012-10-17 13:25:29 -04:00
Daniel Blankenberg
cac074b786
Fix for python2.5.
2012-10-17 12:32:35 -04:00
Dannon Baker
13356dff74
Remove unused imports, fix exception log str(e) (which was actually e imported from another package, not the exception...)
2012-10-16 16:47:31 -04:00
Dannon Baker
fe5fb9a666
Fix test cases failing due to non-reflected password change. This resolves failures of:
...
functional.test_user_info.TestUserInfo.test_010_user_reqistration_multiple_user_info_forms
functional.test_user_info.TestUserInfo.test_015_user_reqistration_single_user_info_forms
functional.test_user_info.TestUserInfo.test_020_edit_user_info
functional.test_user_info.TestUserInfo.test_999_reset_data_for_later_test_runs
2012-10-16 16:43:58 -04:00
Scott McManus
2c20cece2e
Added folder_contents controller and enabled both folder and folder_contents controllers
2012-10-16 16:32:01 -04:00
Daniel Blankenberg
1e55e46201
Performance enhancements for Build custom track for UCSC genome browser tool.
2012-10-16 15:25:01 -04:00
Jeremy Goecks