Greg Von Kuster
f16d27c2d4
Add datasource tool configs for modMine and Ratmine.
2009-12-03 15:33:15 -05:00
Jeremy Goecks
85b6b2047e
Bug fixes for 'insert history' operation in pages.
2009-12-03 14:39:21 -05:00
Enis Afgan
cf643df67d
Added ability for a user to start 64bit cloud instances.
2009-12-03 14:16:50 -05:00
Greg Von Kuster
0e807f13f5
Add support for uploading BAM files.
2009-12-02 20:02:05 -05:00
Kelly Vincent
f446bce0c1
Updated Lastz tests with comments
2009-12-02 15:23:15 -05:00
Nate Coraor
c53e0d626f
Fix static_enabled config option and a bad image path in the index template
2009-12-02 10:58:42 -05:00
Greg Von Kuster
736f36a5ae
Bug fix - add a needed import to ~/datatypes/data.py.
2009-12-02 10:07:21 -05:00
Greg Von Kuster
81bd968bd1
Fixes for lastz_wrapper that includes job splitting, more functional tests, removed incorrectly committed .loc file and committed the .loc.sample file.
2009-12-01 20:16:41 -05:00
Kelly Vincent
606ac644f3
Added some error checking to pileup_parser tool so that it exits with a meaningful message if the user tries to do some 6-column work on a 10-column file, or vice versa.
2009-12-01 16:18:25 -05:00
Guruprasad Anada
10af4c5ccf
Adding back 'wiggle to interval' converter
2009-12-01 11:49:07 -05:00
Jeremy Goecks
a333097860
Improved loading state for AJAXed grids: when grid is loading, gray out table and prevent further user actions.
2009-12-01 11:07:20 -05:00
Enis Afgan
917ad8ac4d
Merge
2009-12-01 09:53:36 -05:00
Jeremy Goecks
598e6630e2
Framework for recording user actions for reports; framework is modelled after event recording. Currently two types of actions are recorded: (a) tagging/untagging and (b) filtering/searching in grids.
2009-11-30 17:53:25 -05:00
Enis Afgan
b962965b64
Merge
2009-11-30 16:47:18 -05:00
Enis Afgan
7f01dc592a
Added ability for a user to add additional storage volume(s) to a running EC2 instance. In this context, a new EBS volume is created, attached to a running instance, and then added to remote zpool. When an instance is shut down and then started back up, all of the associated storage volumes are automatically attached to it and the zpool is imported.
2009-11-30 16:36:38 -05:00
Daniel Blankenberg
87938b9894
Fix MAF to BED tool. This tool should be rewritten to not use a code file, but instead use one of the standard ways to create additional outputs, similar to how maf_to_interval functions.
2009-11-30 15:33:45 -05:00
Daniel Blankenberg
77bd226f2b
When setting metadata externally, substitute a MetadataTempFile object for all populated metadata FileParameters. Fixes the problem with writting to metadata FileParameter files on cluster nodes with read-only database/files directory.
2009-11-30 14:55:30 -05:00
Guruprasad Anada
ed381c7333
Fixed a bug in 'fetch closest features' tool.
2009-11-30 11:59:54 -05:00
Guruprasad Anada
049068730a
Added 'N' to the list of mask characters, as per Melissa's request.
2009-11-30 11:56:58 -05:00
Ramkrishna Chakrabarty
14751d54b5
Fix for request_events table migration script for MySQL & sqlite
2009-11-30 09:35:21 -05:00
Kelly Vincent
1fcafa5a86
Added usage information, added/updated relevant test files, and got all tests working for Lastz
2009-11-30 09:05:28 -05:00
Greg Von Kuster
20628e8381
First pass of the lastz tool wrapper that includes job splitting - works but needs polishing.
2009-11-27 10:53:50 -05:00
Ramkrishna Chakrabarty
d2eb5a388b
Request events & request rejection (resolves issue #221 )
...
- added request_events table
- removed 'state' field in the request table
- added 'new' & 'rejected' request states
- color coded request states in the request grid
Grids framework
- added a confirm flag in grid operations which require confirmation before going through with operation
2009-11-25 14:06:28 -05:00
Jeremy Goecks
7b7ec2b184
Added AJAX functionality to main grid framework. Use the use_async flag to turn on AJAXing in a grid; see the history grid for an example of a grid that uses AJAX. Small changes that are needed to fully employ AJAX for a grid are: (a) using the async_compatible flag to indicate which operations can be AJAXed and which cannot; and (b) ensuring that controller code for grid handles operation names in a case-insensitive manner. Also, there are bug fixes for inserting a history link into a page.
2009-11-24 14:53:19 -05:00
Kanwei Li
e4a4889524
Fix run.sh --reload by requiring Paste before PasteScript
2009-11-23 17:20:01 -05:00
Nate Coraor
a6f934b9cc
Remove old tools from runner config in universe config
2009-11-23 09:21:22 -05:00
Daniel Blankenberg
5927efceff
Remove metadata_source from quality_filter tool output. This will allow this tool to work on the cluster with external metadata and a readonly database/files filesystem. A better overall fix for setting external metadata files is in the works.
2009-11-20 16:22:04 -05:00
Greg Von Kuster
f5bf037191
Rename test files for taxonomy tools and set ftype for test's input datasets.
2009-11-20 15:35:30 -05:00
Kanwei Li
82eef1efcf
Data from UCSC table browser now uses hgta_table for table name. Fixes #67
2009-11-20 15:25:13 -05:00
Kanwei Li
b2bbf68264
update bx_python egg
2009-11-20 12:07:06 -05:00
Greg Von Kuster
a722a2aa0a
Move line count processing from set_peek() methods to set_meta() methods for data types since set_meta can run externally and it does line by line processing in some cases. Added new MetadataElements to the Data, Text, Sequence and Maf classes to handle setting dataset.blurb from stored metadata. Cleaned up a lot of code in the process.
2009-11-20 11:03:41 -05:00
Greg Von Kuster
de8b4d7be5
Eliminate the ability to delete/undelete/purge users until the grid helper can access config settings.
2009-11-20 08:46:49 -05:00
Kanwei Li
fb00e2b7a2
trackster: load block data incrementally, huge performance gains from drawing smaller tiles
2009-11-19 18:55:35 -05:00
Enis Afgan
4c7e009359
Fixed a bug in cloud store update. Also, added method comments to EC2 cloud provider implementation class.
2009-11-19 12:56:24 -05:00
Nate Coraor
6cf823e1ef
Only fix OS X platform name on 2.5, the only version on which it's broken
2009-11-18 16:18:09 -05:00
Kanwei Li
9efa130e6f
revert to sqlite default in universe.sample
2009-11-18 13:45:53 -05:00
Enis Afgan
bcf8c43069
merge
2009-11-18 13:37:41 -05:00
Enis Afgan
82a7e1d9cc
Fixed table migration bug encountered with PostgreSQL.
2009-11-18 13:36:37 -05:00
Jeremy Goecks
405e679191
Tweaks to grid filter UI: (1) added search image/submit button for initiating search and (2) styled text filter criteria.
2009-11-18 11:51:09 -05:00
James Taylor
1c33863991
Change a few foreign keys, this may change behavior of the cloud stuff, needs to be checked.
2009-11-18 10:57:24 -05:00
James Taylor
5b6aeb3231
Another tweak to cloud table order
2009-11-18 10:47:14 -05:00
James Taylor
d10f6f40be
Change cloud table creation order
2009-11-18 10:43:08 -05:00
Jeremy Goecks
1820348d81
Unicode fix: make it possible to display non-acii characters in dataset name.
2009-11-18 09:52:38 -05:00
Jeremy Goecks
03780db05d
merge
2009-11-17 19:07:19 -05:00
Jeremy Goecks
7519604261
'Insert history link' functionality added to pages. A user can select 1 or more histories and create links that point to a view of each history.
2009-11-17 19:06:42 -05:00
Enis Afgan
9312efac12
Fix cloud execution on startup
2009-11-17 16:39:05 -05:00
Enis Afgan
05fb70f48d
merge
2009-11-17 16:16:26 -05:00
Enis Afgan
1bb086c83d
Moved cloud control flag in universe.ini file to appropriate location.
2009-11-17 16:14:54 -05:00
Enis Afgan
af64c352fd
Completed port to SQLalchemy 0.5. Also, fixed couple of bugs, cleaned up cloud provider code, tested w/ EC2.
2009-11-17 15:51:39 -05:00
Ramkrishna Chakrabarty
c73610de9d
Adding grids to forms, requests & request types pages. Resolves issue #231 .
2009-11-17 14:28:34 -05:00
Greg Von Kuster