Khalid Shakir fac9932938 Embedding gsalib source and queueJobReport R scripts in the dist and package jars. ... Moved gsalib and queueJobReport.R to embeddable namespaced locations. Updated packager dependencies/dir to add an @includes which filters the embedded fileset. RScriptExecutor can now JIT compiles the gsalib. RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG. Refactored ProcessController and IOUtils from Queue to Sting Utils. Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count. Replaced uses of some IOUtils with Apache Commons IO. ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown. Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().		2011-10-24 15:58:34 -04:00
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Aligner.xml	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
AnalyzeCovariates.xml	Fix the AnalayzeCovariates packaging.	2011-09-22 11:55:40 -04:00
CreatePackager.xsl	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
GATK-Picard.xml	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GATKEngine.xml	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
GenomeAnalysisTK.xml	Moving AnalyzeAnnotations into the archive because it has outlived its usefulness.	2011-07-02 10:39:53 -04:00
PicardPrivate.xml	Using picard implementations for accessing aggregation directories.	2011-07-18 21:49:03 -04:00
Queue.xml	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00