Commits

Author Commit Message Labels Comments Date
John Chilton
Rework dynamic job runner config so that instead using a rules.py file
John Chilton
First attempt at updated dynamic job runners.
jeremy goecks
Handle Tophat2 fusion-ignore-chromosome parameter correctly.
jeremy goecks
Backbone-ify server-state deferred and use when running tools in Trackster.
jeremy goecks
Add min, max insert size parameters to bowtie2 wrapper.
Nate Coraor
Fix API history undelete, issue #763.
jeremy goecks
Fix bug in setting Bowtie2 parameters.
Greg Von Kuster
Ehancements for automatic installation of tool dependencies when installing tool shed repositories; the enhancements support moving files and changing subdirectories during tool dependency installation.
Ross Lazarus
branch merge
Ross Lazarus
Add some more missing quotes to command line.
Ross Lazarus
Updates to fastqc tool to wrap the user supplied job name in quotes and sanitize to letters/digits only
jeremy goecks
Draw tiles based on region rather than tile index because it provides more flexibility.
jeremy goecks
Visualization infrastructure: (a) Backbone-ify cache and data managers; (b) push parameter value sampling code into Tool objects. Pack scripts.
jeremy goecks
Fix bugs in fetching reference genome data.
smcmanus
XML parsing for applying regular expressions and exit code checking to tools' output
Daniel Blankenberg
Add BAM slicing tool to tool_conf.xml.main.
jeremy goecks
Add preset alignment options to Bowtie2 wrapper and fix default in Tophat2 wrapper.
Greg Von Kuster
Refinements for setting metadata on the entire change log of tool shed repositories.
jeremy goecks
Update default and help for Tophat2 coverage search parameter.
Greg Von Kuster
Fixes for getting updates to installed tool shed repositories.
Greg Von Kuster
Fix for rendering the url for cloning a tool shed repository.
Ross Lazarus
Added __admin_users__ as a parameter so tools can check __user_email__ and refuse to run unless
Ross Lazarus
Adding a new datatype to datatypes_conf.xml.sample - toolshed compatible gzips created by a new automated
jeremy goecks
Foundation for parameter sweeping visualization.
Greg Von Kuster
Fixes for setting metadata on tool shed repoistories.
Greg Von Kuster
Fixes for handling tool shed repository files that have been renamed or deleted.
Greg Von Kuster
Refinements for locating desired files within a tool shed repository manifest and setting metadata on tool shed repositories.
Init Hello
Made genome tool backwards compatible with python 2.5.
jeremy goecks
Place all JavaScript visualization code under static/scripts/viz directory.
jeremy goecks
Clarify inputs for forward, reverse reads in Tophat2 wrapper.
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