Jeremy Goecks
f3066fc658
Backbone-ify server-state deferred and use when running tools in Trackster.
2012-06-08 15:36:02 -04:00
Jeremy Goecks
0c12da85ba
Add min, max insert size parameters to bowtie2 wrapper.
2012-06-08 14:03:41 -04:00
Nate Coraor
193172d816
Fix API history undelete, issue #763 .
2012-06-08 13:52:06 -04:00
Jeremy Goecks
a08c0c03ce
Fix bug in setting Bowtie2 parameters.
2012-06-08 13:48:37 -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
Ross Lazarus
15ef69b7d2
branch merge
2012-06-08 08:31:56 +10:00
Ross Lazarus
c14fcf5ea0
Add some more missing quotes to command line.
2012-06-08 08:28:35 +10:00
Ross Lazarus
9fbf7007c7
Updates to fastqc tool to wrap the user supplied job name in quotes and sanitize to letters/digits only
...
Some downstream problems from ( characters reported today but probably needs deeper sanitizing
2012-06-08 08:26:09 +10:00
Jeremy Goecks
5deadd39cd
Draw tiles based on region rather than tile index because it provides more flexibility.
2012-06-07 17:43:22 -04:00
Jeremy Goecks
f8f06c3706
Visualization infrastructure: (a) Backbone-ify cache and data managers; (b) push parameter value sampling code into Tool objects. Pack scripts.
2012-06-07 16:47:06 -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
Daniel Blankenberg
af7cf227de
Add BAM slicing tool to tool_conf.xml.main.
2012-06-07 10:06:43 -04:00
Jeremy Goecks
63fec8c332
Add preset alignment options to Bowtie2 wrapper and fix default in Tophat2 wrapper.
2012-06-06 15:27:59 -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
Jeremy Goecks
d802171ccb
Update default and help for Tophat2 coverage search parameter.
2012-06-06 14:42:21 -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
Ross Lazarus
51e71a325c
Adding a new datatype to datatypes_conf.xml.sample - toolshed compatible gzips created by a new automated
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script wrapper.
2012-06-06 12:08:55 +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
5ba3cb6553
Place all JavaScript visualization code under static/scripts/viz directory.
2012-06-04 12:26:52 -04:00
Jeremy Goecks
f7cfc540bd
Clarify inputs for forward, reverse reads in Tophat2 wrapper.
2012-06-04 09:29:51 -04:00
Jeremy Goecks
1774b76b32
Add entry for Tophat2 indices to tool data table.
2012-06-04 09:07:19 -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
51312405f4
Add Bowtie2 preset options to Tophat2 wrapper.
2012-05-31 11:08:24 -04:00
Jeremy Goecks
2b023cc95f
Tophat2 wrapper updates: (a) use bowtie2-build; (b) add option to report discordant pairs; (c) update tests.
2012-05-31 10:08:13 -04:00
Jeremy Goecks
27f7aa9fde
Clearer explanation and help for default vs. full parameter settings.
2012-05-30 19:47:40 -04:00
Jeremy Goecks
52d4e3f40d
Fix compatibility issue with 9765176c63f7
2012-05-30 18:09:26 -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
Jeremy Goecks
988313826f
Fix bug in showing/hiding filters in Trackster.
2012-05-30 09:39:59 -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
c3e6472d1b
Move icons from trackster.css to base.css for general usage.
2012-05-28 12:05:20 -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