Daniel Blankenberg
a01df218d7
Update CCAT to version 3.0.
2011-03-16 10:41:38 -04:00
Kanwei Li
612b35e611
Small tweaks to custom builds
2011-03-16 09:01:57 -04:00
Kanwei Li
2c06d0246d
Improved custom builds UI. Better help text explaining len file format. Now split on last whitespace instead of tab only so that len info can be typed into the box directly.
2011-03-15 23:40:53 -04:00
Dannon Baker
082bd83a5c
Fix for example workflow api script failing when the requested library doesn't exist and an attempt is made to create it.
2011-03-15 15:39:35 -04:00
Greg Von Kuster
32fa542fca
Allow Importing items from a history to replace a library dataset with a new version.
2011-03-15 14:43:06 -04:00
Greg Von Kuster
7640af8e06
Don't alter the contents of a file while uploading to a data library if using the filesystem_paths option. This partially resolves the issue where a supposedly sorted BAM file was being resorted upon upload to a data library when using this option. A better imlementation of determining whether a BAM file has been sorted (so that it does not get resorted) remains to be done.
2011-03-15 09:38:29 -04:00
Daniel Blankenberg
5fc793c8f2
Allow upload to function on https URLs.
2011-03-14 23:01:11 -04:00
Kanwei Li
dcfa7af7cc
trackster: Fix BAM reads without cigar string (assume all match); datasets added into a new track browser will now index immediately instead of after changing a chrom
2011-03-11 17:54:06 -05:00
Kanwei Li
6d8eb1015e
Include
2011-03-11 15:57:06 -05:00
Greg Von Kuster
df6f94b1d0
Per request from Peter Cock, turn the "Copy data into Galaxy?" check box into a select list that clarifies the behavior. The default is to copy files into Galaxy.
2011-03-11 14:56:11 -05:00
Kanwei Li
2b83ae36b9
trackster: Suppress cython warning message causing bam_to_summary_tree to fail. Fix for chroms without 'chr' in front not being displayed
2011-03-11 13:36:29 -05:00
Greg Von Kuster
c650958915
Apply a corrected version of the patch from Peter Cock that flips the  "Preserve directory structure?" setting when uploading library datasets from filesystem paths.
2011-03-11 10:01:54 -05:00
Greg Von Kuster
4e691cffa3
Apply patch from Ry4an Brase to correct "NoneType dereference on the jobs view" issue.
2011-03-11 09:16:16 -05:00
Jeremy Goecks
ebab920cca
Trackster: access to datasets is based on accessibility, not ownership.
2011-03-10 17:30:35 -05:00
Jeremy Goecks
0c2b732e8e
Make shared visualizations work again and pack trackster.js
2011-03-10 16:42:34 -05:00
Kanwei Li
4d45e6f5b2
merge
2011-03-10 16:11:49 -05:00
Kanwei Li
dd4838772d
Make workflow run_complete.mako modern
2011-03-10 16:09:03 -05:00
Kelly Vincent
833478bbbd
Added two more builds to the manual builds list
2011-03-10 16:08:39 -05:00
Greg Von Kuster
0e79bf2632
Add a checkbox to the Create Group page that if checked will create a new Role with the same name. This provides a similar feature the the existing checkbox on the Create Role page.
...
However, the behavior is now changed such that new associations are created when the checkbox is checked whereas before, only the Group or Role objects with the same name were created, but not associated with anything.
This code was very old, so I did some cleanup / improvements as well. Functional tests enhanced to reflect changes.
2011-03-10 15:48:00 -05:00
Daniel Blankenberg
0e0fd1577d
Allow composite datatype datasets to be populated in the Upload tool from files that were uploaded to the Galaxy FTP server.
2011-03-10 15:20:40 -05:00
Kelly Vincent
b5ee9ee8c7
Modified script that adds manual builds to add build even if chrom length details not present; added a few new manual builds
2011-03-10 13:28:33 -05:00
Ramkrishna Chakrabarty
d26b62573c
Extending sample search to include search using form fields. Resolved #489
2011-03-09 15:33:04 -05:00
Greg Von Kuster
a5ea34e29a
Add functional tests to cover some recent new library features, and a couple of miscellaneous UI improvements.
2011-03-09 14:50:54 -05:00
Jeremy Goecks
82ef98f15c
Fix bugs in GFFReaderWrapper so that GFF3 files are read properly. Add GFF3 test to gff_filter_by_feature_count.
2011-03-09 14:22:10 -05:00
Jeremy Goecks
86b7194bff
Use GFFReaderWrapper in gff_filter_by_feature_count tool in order to leverage support for GTF, GFF, and GFF3 found in reader wrapper. This also simplifies the tool considerably.
2011-03-08 19:01:59 -05:00
Kelly Vincent
a4f910c730
Update SRMA test files so that functional tests pass
2011-03-08 16:17:09 -05:00
Greg Von Kuster
b94de80659
Add the ability to move data library items within a data library or between data libraries.
2011-03-08 15:50:19 -05:00
Ramkrishna Chakrabarty
a97da4abcf
Add import statement for binascii
2011-03-08 14:35:26 -05:00
Ramkrishna Chakrabarty
5bfdb9443b
Added the postgres9 json sniffnfix method to the migration script instead of importing it from custom_types.py
2011-03-08 14:08:07 -05:00
Ramkrishna Chakrabarty
a20d7738b6
Fixes the data corruption caused in the form_values table (content field) by the migrate script 65.
2011-03-08 12:42:26 -05:00
Nate Coraor
a221548e8f
An uninitialized value in R's PDF driver was causing it to sometimes randomly add a few elements to PDF outputs. The bug has been fixed in the buildbot environment and these changes account for that fix.
2011-03-08 11:17:57 -05:00
Jeremy Goecks
b64c880315
Remove debugging statement.
2011-03-08 10:26:52 -05:00
Jeremy Goecks
6d4519f363
Trackster: enable full keyboard navigation via arrow keys using jquery.scrollTo plugin.
2011-03-08 10:04:39 -05:00
Jeremy Goecks
23a5d3588a
Trackster: remove form from nav controls so that enter key works properly and sets the chrom/low/high.
2011-03-07 22:00:50 -05:00
Jeremy Goecks
0030c2c810
Fix bug in output for gff_filter_by_feature_count tool.
2011-03-07 15:53:31 -05:00
Jeremy Goecks
4b78ad9765
Fix bug in GFF/GTF feature parser: new feature starts when transcript_id _or_ gene_id changes.
2011-03-07 15:40:24 -05:00
Guruprasad Anada
595fa98ef4
merge
2011-03-07 13:47:16 -05:00
Guruprasad Anada
4a81da484c
Updated tool help for microsatellite birth/death tools.
2011-03-07 13:30:37 -05:00
Nate Coraor
c83d376e42
If the referer is the logout page, redirect to base analysis interface after login instead of back to the logout page. Fixes issue #486 .
2011-03-07 13:30:29 -05:00
Jeremy Goecks
3d70cf047e
Show masthead links to Published Visualizations and Published Pages only if tracks/pages are enabled.
2011-03-07 11:43:51 -05:00
Greg Von Kuster
75c606d961
Remove reference to setup.sh which is no longer used.
2011-03-07 10:02:39 -05:00
Jeremy Goecks
ab50ae5b55
Trackster: another pass on reads insertion display. Fixed bugs, add menu item to show/hide insertions, and improve display of insertions. Pack scripts.
2011-03-05 18:33:06 -05:00
Dannon Baker
95545a8973
Add basic security to workflows api.
2011-03-05 16:32:41 -05:00
Dannon Baker
5b2f58bb14
Adjust ColumnListParameter tests to account for the new return from History.add_dataset.
2011-03-05 16:15:55 -05:00
Dannon Baker
9655aa55f5
Set workflow scripts ugo+x, like the others in scripts/api.
2011-03-05 12:44:32 -05:00
Dannon Baker
159c25eb68
Example script that uses the API to watch a folder for inputs, upload (filepath upload) those to a data library, and then execute a specified workflow on them.
2011-03-05 12:28:16 -05:00
Dannon Baker
e62494e2b0
Initial commit of workflows API. Supports simple execution, multiple input datasets. Does not support runtime tool parameter modification.
2011-03-05 11:47:12 -05:00
Dannon Baker
77eace152f
Removed invalid parameter in History.add_dataset, added return of dataset to the method.
...
Add APIItem to StoredWorkflow.
2011-03-05 11:31:41 -05:00
Jeremy Goecks
259ec2d649
Trackster: add another parameter to draw() method that determines whether to clear old tiles immediately or after new tiles have been drawn. This parameter enables draw() to clear a track quickly (e.g. when scrolling fast) or slowly (e.g. when using filters). Also included is a long comment about why clearing tiles after often fails and ways to address this issue.
2011-03-04 15:22:17 -05:00
Jeremy Goecks
35a5196daa
Trackster: refactor filtering functionality out of draw() method and do use CSS classes for information transfer. Also remove unused menu code.
2011-03-04 14:29:19 -05:00
Daniel Blankenberg