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
1af6e33966
Add a 'subclass' flag to datatype definitions in datatypes_conf.xml that allows dynamic creation of a subclass.
...
For example, to create a datatype that has the attributes of a Tabular file, but is more 'specific':
<datatype extension="more_than_tabular" type="galaxy.datatypes.tabular:Tabular" subclass="True" />
2011-03-04 10:28:04 -05:00
Daniel Blankenberg
e7f3e397b6
Add missing bowtie test file from changeset 5157:7a9476924daf
2011-03-04 10:02:01 -05:00
Ramkrishna Chakrabarty
cef8e1cc70
Backed out of changeset 5173:ac6b14ffc984
2011-03-04 09:59:06 -05:00
Ramkrishna Chakrabarty
3e7e8c2238
Fixes the data corruption caused in the form_values table (content field) by the migrate script 65.
2011-03-04 07:28:23 -05:00
Kanwei Li
0472e3eb6e
trackster: Refactor to use one central tile_data method instead of having separate get_data methods for each type of track.
2011-03-03 21:06:33 -05:00
Jeremy Goecks
2864d89238
Trackster: refactor filters code to use functions and styles from tool parameters.
2011-03-03 17:40:35 -05:00
Kanwei Li
cb076fdd9a
trackster: Fix summary_tree and error messages
2011-03-03 16:32:04 -05:00
Jeremy Goecks
52acff3112
Trackster: refactor and enhance track popup menus so that menu items can be dynamically updated. Improve menu descriptions for showing/hiding filters and tools.
2011-03-03 15:38:48 -05:00
Nate Coraor
e3f970a36f
Use lines_diff on the pdf outputs of various R-based tools.
2011-03-03 12:21:44 -05:00
Nate Coraor
19236474c4
Cause lines_diff on pdf test outputs to only count the lines of a pdf which are not already ignored.
2011-03-03 12:21:22 -05:00
Kelly Vincent
eae96d79be
Updated first test output file for SRMA wrapper to get it passing
2011-03-03 12:03:41 -05:00
Jeremy Goecks
b3edc1b905
Trackster bug fixes for drawing feature tracks in squish and dense mode.
2011-03-03 11:47:10 -05:00
Nate Coraor
a69fd37c10
New test data output for histogram tool.
2011-03-03 08:29:15 -05:00
Kanwei Li
dc108dd26f
trackster: reorganize drawing so that it's callback based. Now it will only draw read tracks after reference sequence is downloaded, if applicable.
2011-03-02 18:03:51 -05:00
Jeremy Goecks
c01a15b638
Set message type to error when history deletion fails due to sharing. Fixes #477
2011-03-02 17:31:09 -05:00
Jeremy Goecks
ebf81092c4
Trackster: make visual analytics code compatible with HDA/LDDA changes.
2011-03-02 17:15:08 -05:00
Nate Coraor
8ba82ff34e
Generalize setup of chrom length files for buildbot.
2011-03-02 16:21:36 -05:00
Nate Coraor
136bae9300
Fix symlink to microbial_data.loc in buildbot setup.
2011-03-02 16:20:16 -05:00
Nate Coraor
ea0e8ead22
Fix the qual_stats_boxplot and quality_score_distribution tests again, hopefully
2011-03-02 13:46:07 -05:00
Daniel Blankenberg
4685ec3f8a
Enhance Bowtie wrapper to accept non-sanger variant FASTQ files.
2011-03-02 11:40:58 -05:00
Daniel Blankenberg
2935741194
Allow FromParamToolOutputActionOption and ParamValueToolOutputActionOptionFilter to access attributes of parameter values.
2011-03-02 11:34:36 -05:00
Daniel Blankenberg
ad3f55b5b0
Allow DataToolParameter to be filtered on attributes other than dbkey.
2011-03-02 11:34:03 -05:00
Greg Von Kuster
4bdc069c4d
Clarify what's being searched in the tool shed.
2011-03-02 09:59:24 -05:00
Ramkrishna Chakrabarty
bdb4ec4505
Fix for vcf_extract tool test
2011-03-02 09:40:10 -05:00
Dannon Baker
a9548d1a07
Remove ftype from mosaik/freebayes test outputs.
2011-03-02 08:38:19 -05:00
Nate Coraor
0411837b7b
Drop the ftype attribute from tophat test outputs
2011-03-02 08:28:30 -05:00
Greg Von Kuster