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12 Commits (86305a5dcfc058a8a31bb27aaefe2576c993a3aa)

Author SHA1 Message Date
David Roazen 442d33ba18 Enable testing of the jars produced by the packaging system. 
-Added targets to run unit and integration tests on the fully-packaged GATK jar,
and pipeline tests on the fully-packaged Queue jar. Once enabled in Bamboo,
these will provide greatly-enhanced protection against breakage in the binary
release.

-Unconditionally include all of the subset of org.broadinstitute.sting
included in the intermediate jars GenomeAnalysisTK.jar, StingUtils.jar,
etc. in the final, fully-packaged jar. This:
    * is necessary to get tests to run on the fully-packaged jar
    * decreases the chances of a class that is a runtime-only
      dependency getting left out of the binary release
    * only slightly increases the size of the binary release
      (before: 9352465 bytes, after: 10985482 bytes)
 2011-10-14 03:08:28 -04:00
Khalid Shakir b090751f62 Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths. 
Updates to HybridSelectionPipeline:
- Added annotations back via snpEff
- Minor updates to VQSR paths and lowered memory
 2011-09-27 14:33:57 -04:00
Matt Hanna 059cdcb1be Changing packaging system path for GATK-only Tribble codecs. 2011-09-26 14:58:19 -04:00
Eric Banks 5e06a45628 Fix the AnalayzeCovariates packaging. 2011-09-22 11:55:40 -04:00
Eric Banks 4e116760f4 Removing some old cruft from the packages dir. Updating AnalyzeCovariates to include all Covariates. 2011-09-12 15:09:25 -04:00
Khalid Shakir 1f8fc4a041 Added edu.mit.broad.picard to Queue packaged jar. 
Added hack to workaround EDU.oswego namespace and staging on mac case-insensitive filesystems.
 2011-07-23 14:40:29 -04:00
Khalid Shakir 9b446020f9 Using picard implementations for accessing aggregation directories. 
Added more utilities to PicardPrivate.
Revved picard.
 2011-07-18 21:49:03 -04:00
David Roazen 8a78414432 Removed TileCovariate as a dependency for AnalyzeCovariates.jar 2011-07-11 12:10:11 -04:00
Ryan Poplin 5faf40b79d Moving AnalyzeAnnotations into the archive because it has outlived its usefulness. 2011-07-02 10:39:53 -04:00
Khalid Shakir b6bc64a0c8 Cleanup of the utils.broad package. 
Using Picard IoUtils on sample names.
 2011-07-01 20:47:03 -04:00
David Roazen 4b17f34640 Fixes to the packaging system to work with the new directory structure. 
Also added a few R scripts to the list of files to include in the resources
directory of the binary distribution, at Ryan's request.
 2011-06-30 18:27:17 -04:00
David Roazen 3c9497788e Reorganized the codebase beneath top-level public and private directories, 
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
 2011-06-28 06:55:19 -04:00