Nate Coraor
193172d816
Fix API history undelete, issue #763 .
2012-06-08 13:52:06 -04:00
Greg Von Kuster
ab9afd1af2
Ehancements for automatic installation of tool dependencies when installing tool shed repositories; the enhancements support moving files and changing subdirectories during tool dependency installation.
2012-06-08 11:46:29 -04:00
Jeremy Goecks
9101867e13
Fix bugs in fetching reference genome data.
2012-06-07 14:16:26 -04:00
Scott McManus
2f991f2f84
XML parsing for applying regular expressions and exit code checking to tools' output
2012-06-07 10:45:01 -04:00
Greg Von Kuster
a8a3c23941
Refinements for setting metadata on the entire change log of tool shed repositories.
2012-06-06 15:15:15 -04:00
Greg Von Kuster
44fa0ff880
Fixes for getting updates to installed tool shed repositories.
2012-06-06 13:26:15 -04:00
Greg Von Kuster
dfd49c1999
Fix for rendering the url for cloning a tool shed repository.
2012-06-06 09:48:15 -04:00
Ross Lazarus
85e2a3a5c9
Added __admin_users__ as a parameter so tools can check __user_email__ and refuse to run unless
...
being invoked by a local admin - useful for any potentially dangerous tools.
2012-06-06 14:02:41 +10:00
Jeremy Goecks
cc9381d436
Foundation for parameter sweeping visualization.
2012-06-05 17:10:23 -04:00
Greg Von Kuster
a0c13aa554
Fixes for setting metadata on tool shed repoistories.
2012-06-05 14:59:42 -04:00
Greg Von Kuster
6db0c8162a
Fixes for handling tool shed repository files that have been renamed or deleted.
2012-06-05 12:51:54 -04:00
Greg Von Kuster
c78547ea7d
Refinements for locating desired files within a tool shed repository manifest and setting metadata on tool shed repositories.
2012-06-05 11:15:14 -04:00
Dave Bouvier
1ab5ee3756
Made genome tool backwards compatible with python 2.5.
2012-06-04 13:18:58 -04:00
Jeremy Goecks
76ee8bb680
Merge
2012-06-03 23:09:08 -04:00
Jeremy Goecks
06934836a8
Fix import to be compatible with previous changeset.
2012-06-03 23:07:54 -04:00
Jeremy Goecks
e344d5e62a
Enable Genome objects and chromosome information to be dictified.
2012-06-03 13:52:12 -04:00
Jeremy Goecks
bb7c69f247
More support for genomes as first-class objects: (a) add genomes API; (b) fix bugs in providing genome data.
2012-06-03 12:19:30 -04:00
Jeremy Goecks
55a1ccb01c
Enhance genome support: (a) make genome information available in Galaxy app and (b) refactor genome code out of visualization mixin and into Genome objects.
2012-06-03 11:08:45 -04:00
Greg Von Kuster
65ee79a0f0
Fix for finding the desired file within a specified change set of a tool shed reposity manifest.
2012-06-01 15:37:38 -04:00
Greg Von Kuster
43f98b1969
1) Enhance the InstallManager to provide the installer the ability to choose to install tool dependenceis (or not) rather than automatically installing them.
...
2) Persist changes to the tool_data_table_conf.xml file only if within the Galaxy webapp.
3) Apply the 1-liner fix from change set 9ffef0de07f5 in Peter van Heusden's pull request which fixes a problem where the __init__ tests if config.database_connection is None.
2012-06-01 14:51:41 -04:00
Jeremy Goecks
bc798cef1e
Use backbone to save trackster visualizations.
2012-05-30 16:37:51 -04:00
Greg Von Kuster
ccaf86aad9
Fixes for handling tool shed repositories that include tool_data_table_conf.xml.sample files. The fixes apply to determining if the tool is valid in the tool shed and also to the Galaxy environment when the tool shed repository is installed.
2012-05-30 16:00:18 -04:00
Greg Von Kuster
45b1158e59
Load datatype converters and display appliations included in installed tool shed repositories after the app's toolbox has been inititlaized.
2012-05-30 09:46:25 -04:00
Nate Coraor
329fecda5d
Handle spaces between commas in admin_users
2012-05-30 10:31:56 +02:00
Greg Von Kuster
626f710b1a
Fixes for loading a tool in a tool shed repository.
2012-05-29 14:46:02 -04:00
Jeremy Goecks
6572730fdd
Visualization: (a) rename circos viz 'circster' and (b) foundational work for circster and backbone-visualization integration. Also pack scripts.
2012-05-28 12:10:04 -04:00
Jeremy Goecks
dcd4e48084
Include 'mixin' in names of many common controller mixins.
2012-05-27 16:09:16 -04:00
Jeremy Goecks
da17e4c5b6
Support for saving and validating different visualization types.
2012-05-27 15:54:32 -04:00
Jeremy Goecks
d66b5d0e78
Provide generic support for saving visualizations.
2012-05-27 12:34:52 -04:00
Jeremy Goecks
587727ce9e
Infrastructure for managing visualizations: (a) support for creating multiple types of visualizations; (b) a placeholder visualization API controller; (c) abstract visualization creation so that it can be reused in multiple controllers.
2012-05-25 18:23:43 -04:00
Jeremy Goecks
97650ce691
Partial implementation of Circos visualization using D3.
2012-05-25 15:13:25 -04:00
Ross Lazarus
093144b1cd
Reverse order of job manager and instance in warning
2012-05-25 15:48:49 +10:00
Ross Lazarus
32900a81d4
Fix for bogus double negative compare - allows job management from admin screen when only one job manager running
2012-05-25 15:40:44 +10:00
Greg Von Kuster
cf2ab42fea
Fix a typo in the community common cntroller.
2012-05-24 16:47:25 -04:00
Greg Von Kuster
442b64d00f
Enhance setting metadata on tool shed repositories tha tinclude tools that require entries in the tool_data_table_conf.xml file.
2012-05-24 16:36:32 -04:00
Jeremy Goecks
df28aec040
Full and proper sorting for GTF datasets: sort by, in order, transcript_id, chrom, and start.
2012-05-24 13:26:48 -04:00
Nate Coraor
db3025b805
Add ssh egg and fix a requirement for the Tool Shed.
2012-05-24 10:05:55 -04:00
Dannon Baker
d98dc0da47
History API undelete bug pointed out by Ed Kirton. Resolves BB Issue #763 .
2012-05-24 08:18:49 -04:00
Greg Von Kuster
d5d3e831f1
Re-engineer the process for defining valid tool shed repository changeset revisions and add support for automatically installing and building tool dependencies for tools included in tool shed repositories being installed into a local Galaxy instance. Tool dependencies will be uninstalled if the repository is uninstalled.
2012-05-23 14:23:28 -04:00
Dave Bouvier
3dc18e1dd7
Improved display of genome download/index status.
2012-05-22 11:13:57 -04:00
Jeremy Goecks
8aeb11b1e4
Add flexibility when getting summary tree data.
2012-05-21 23:38:40 -04:00
Jeremy Goecks
e4b014ffa3
Summary tree code tending: add todos and comments, remove version.
2012-05-21 19:08:37 -04:00
Jeremy Goecks
ba255221d3
Trackster: better comments and help text.
2012-05-21 12:42:53 -04:00
Jeremy Goecks
9fbf9a4ab3
Add missing import.
2012-05-21 12:10:55 -04:00
Jeremy Goecks
3371b095bc
Update comments and coding conventions in Trackster code.
2012-05-21 12:10:30 -04:00
Dave Bouvier
5ece871d40
Added option to download pre-built indexes from galaxy servers.
2012-05-18 09:50:35 -04:00
Jeremy Goecks
b261bc7335
Do not use tabix for GFF/GTF because tabix is woefully naive about these data formats.
2012-05-15 10:17:44 -04:00
Jeremy Goecks
7b5f7b25df
Remove genomes initialization code because it's no longer needed.
2012-05-15 09:17:36 -04:00
Jeremy Goecks
db84128c8f
Refactor genome build status and information out of tracks controllers and into own object.
2012-05-11 19:27:30 -04:00
Jeremy Goecks
9c4d8cf2ea
Merged in fbacall/galaxy-central-myexp-integration (pull request #45 )
2012-05-10 16:27:33 -04:00
Nate Coraor