5 Commits (ff26f2bf688048bbd6e2b9ffcf31cedce4fa99dd)

Author	SHA1	Message	Date
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
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
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	b6bc64a0c8	Cleanup of the utils.broad package. ... Using Picard IoUtils on sample names.	2011-07-01 20:47:03 -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