David Roazen 9c6bccfd8b build system overhaul ... * Added support for a protected directory whose contents are only made public in binary form * Simplified and reorganized build.xml to improve readability and maintainability * build.xml now autodetects most build properties: -Includes private/protected if they exist -No more STING_BUILD_TYPE or specialized targets for public-only, etc. * Build targets have changed! There are now two main build options: "ant" build everything (GATK and Queue) "ant gatk" build just the GATK It was too hard to build everything before -- now it is the default. * To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line. Much better than the old comment/uncomment method!		2012-05-17 15:16:29 -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	No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.	2011-10-27 14:17:07 -04:00
CreatePackager.xsl	build system overhaul	2012-05-17 15:16:29 -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	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
GenomeAnalysisTK.xml	build system overhaul	2012-05-17 15:16:29 -04:00
PicardPrivate.xml	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
Queue.xml	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00