Commits

Author Commit Message Labels Comments Date
jeremy goecks
Trackster: reset filters when they are hidden.
jeremy goecks
Trackster: enable dynamic filters to be run on complete dataset using filter tools.
Kelly Vincent
Updated help section of BWA wrappers to include tags for the RG header record type
Daniel Blankenberg
Add GATK tool-data to buildbot_setup.sh links.
Daniel Blankenberg
Have GATK file listings written as html, be sorted.
Nate Coraor
Fix test output for picard_ARRG.
Nate Coraor
Add a method to add manual builds to buildbot runs.
Daniel Blankenberg
Allow gatk_wrapper.py to run in versions of python<2.6.
Kanwei Li
trackster: Fix border and error not lining up at right place
jeremy goecks
Add support for comment handling to gff_to_interval_index tool.
jeremy goecks
Relax diff calculation for Cuffdiff test to account for non-deterministic output.
Kanwei Li
Show details: now works even when tool is obsolete. Show inheritance chain where the dataset came from if it was copied from a history or library
Kelly Vincent
Updated SRMA to properly set dbkey and changed functional tests so that they can handle a single line difference for the SRMA version number tag
Daniel Blankenberg
Some minor fixes for 5537:1a379a0f2ecc.
Daniel Blankenberg
First pass at adding some GATK tools. Included tools are "Realigner Target Creator", "Indel Realigner", "Count Covariates", "Table Recalibration", "Analyze Covariates" and "Unified Genotyper". These tool integrations should be considered beta: changes that will not be backwards-compatible with workflows and re-run functionality should be expected. TODO: A few new datatypes have been declared, but exist in name only (subclasses of Text defined only in datatypes_conf.xml), these should be refined to be true datatypes, with proper peeks, sniffing, metadata, etc. Help sections need work. HTML listing of files in e.g. Analyze Covariates should be prettified. Other items not listed.
Daniel Blankenberg
Add a "contains" compare type to functional tests. Enables simple checking for substrings in a test output file, on a line-by-line basis. TODO: Enhance to enforce order.
Daniel Blankenberg
Fix for expand grouping to allow toolbox tests to use the default parameter value.
Daniel Blankenberg
Have MACS peak caller wrapper use return code to set error state.
Ross Lazarus
added all_fasta.loc to buildbot - needed for picard tests
Ross Lazarus
relax number of lines_diff in insertsize test
Daniel Blankenberg
Fixes for Picard: ReorderSam.
Kelly Vincent
merge
Kelly Vincent
Updated Freebayes to set dbkey on output file
Kelly Vincent
BWA enhancements: added new options to support v. 0.5.9 (-n and -r for samse/sampe and -N for sampe only); fixed dbkey setting; set Sam header suppression off by default
Kelly Vincent
Sam header suppression made optional in BFAST and default set to off for BFAST and Bowtie. Fixed dbkey setting on outputs for for BFAST, Bowtie, Mosaik. Fixed sorting of built-in builds for these tools so ordered by pretty name.
Kelly Vincent
Updated sam-to-bam to properly assign output dbkey; enhanced sam-to-bam and bam-to-sam functional tests
Ross Lazarus
branch merge
Ross Lazarus
small changes to fix test outputs for insertsize and bamindex
jeremy goecks
Update cuffdiff wrapper and test data for v1.0.1
Kelly Vincent
merge
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