Commit Graph

5 Commits (f9f8589692fece0185a7e8e059b75ee4672d1c8d)

Author SHA1 Message Date
Khalid Shakir aae61767c6 queueJobReport now compresses PDF when running R 2.13+.
Updated PostCallingQC.scala's VE and R to include missense to silent ratio and plot.
2012-01-10 17:32:30 -05:00
Mark DePristo 5383c50654 Protect ourselves when iteration is present but there's only a single iteration in queueJobReport.R 2011-12-19 10:08:38 -05:00
Mark DePristo 50c4436f90 scales=free shows variance within analysis better 2011-12-07 14:09:32 -05:00
Mark DePristo e17a1923fb Plots runtimes by analysis name and exechosts
Useful to understand the performance of analysis jobs by hosts,
and to debug problematic nodes
2011-12-07 09:24:47 -05:00
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