kshakir e21a66d876 Updated the Queue GATK generator and packaging to include more dependencies for fullCallingPipeline.q. ... Set the -bigMemQueue in the FullCallingPipelineTest to GSA to avoid waiting for the week queue when it is busy. Fixed the package definition of PipelineTest so that scalac won't recompile it every time. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4755 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-30 15:29:40 +00:00
..
Aligner.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
AnalyzeConcordance.xml	Added a playground concordance analyzer for summarizing VariantEval across a group.	2010-02-22 20:28:52 +00:00
AnalyzeCovariates.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
CreatePackager.xsl	Tweak the layout of the resulting .tar.bz2 a bit.	2010-01-27 22:07:37 +00:00
FindContaminatingReadGroups.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
GATK-Picard.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
GATKResources.xml	/broad/1KG doesn't exist	2010-10-06 12:54:38 +00:00
GenomeAnalysisTK.xml	Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release.	2010-11-18 02:33:45 +00:00
IndelGenotyper.xml	Bringing IndelGenotyper back to life	2010-02-03 20:12:49 +00:00
LocalRealignmentAroundIndels.xml	Since IntervalCleaner is gone for good, it is sensible to update the package to refer to the new IndelRealigner instead	2010-02-24 16:42:56 +00:00
PicardPrivate.xml	Update to the latest rev of the picard sharding patch. Includes updates reflecting	2010-06-06 20:33:21 +00:00
QualityScoresRecalibration.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
Queue.xml	Updated the Queue GATK generator and packaging to include more dependencies for fullCallingPipeline.q.	2010-11-30 15:29:40 +00:00
RMDIndexer.xml	include the codecs into the RMD indexer that are available in the GATK, not just Tribble	2010-11-11 06:35:04 +00:00
UnifiedGenotyper.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
VariantAnnotator.xml	Include all standard annotations	2010-10-11 20:52:08 +00:00
VariantEval.xml	Add CountFunctionalVariants to local release (for firehose)	2010-07-17 01:36:16 +00:00
VariantFiltration.xml	Temporary solution: add the commons logging implementation to the VariantFiltration package. Downstream solution is described in GSA-262.	2010-01-23 01:46:18 +00:00
VariantRecalibration.xml	VariantOptimizer package is moved to core, renamed as VariantRecalibration, and added to the binary release package. VariantOptimizer walker is renamed to GenerateVariantClustersWalker and ApplyVariantClustersWalker renamed to VariantRecalibrator. Integration tests added, performance tests still to be done.	2010-05-28 18:20:18 +00:00