gatk-3.8

Commit Graph

Author	SHA1	Message	Date
Mauricio Carneiro	2a4ccfe6fd	Updated all JAVA file licenses accordingly GSATDG-5	2013-01-10 17:06:41 -05:00
Khalid Shakir	b80d407dc7	No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. Other minor cleanup.	2011-10-27 14:17:07 -04:00
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

Author

SHA1

Message

Date

Mauricio Carneiro

2a4ccfe6fd

Updated all JAVA file licenses accordingly

GSATDG-5

2013-01-10 17:06:41 -05:00

Khalid Shakir

b80d407dc7

No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.

Other minor cleanup.

2011-10-27 14:17:07 -04:00

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

3 Commits (fce448cc9e8fac6aa950a1ccd42140f2cbeb598e)