kshakir 673fa841a4 Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader. ... Removed obsolete usages of PackageUtils with updated PluginManager. Ported Queue interval utilities written in scala over to Sting's java IntervalUtils. Added a very basic intergration test to ensure that the fullCallingPipeline.q compiles. Added options to specify the temporary directories without having to use -Djava.io.tmpdir (useful during the above integration test). While adding tempDir added options to specify the run directory from the command line, for example "-runDir v1". Upgraded to scala 2.8.1 and updated calls to deprecated functions. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4661 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-12 20:14:28 +00:00
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CollectionUtils.scala	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
CommandLineJob.scala	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00
EmailMessage.scala	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00
EmailSettings.scala	Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline.	2010-10-14 15:58:52 +00:00
IOUtils.scala	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00
JobExitException.scala	Instead of the pipeline's cleaner only writing BAMs with the target intervals, now pulling the list of contigs from the target intervals and outputing reads in those contigs.	2010-10-22 22:22:30 +00:00
Logging.scala	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
LsfJob.scala	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00
LsfKillJob.scala	Wrapping ScatterGatherableFunctions with a facade instead of using slower clone library. Will require keeping Clone's facade code in sync with CommandLineFunction but runs *much* faster.	2010-10-07 01:19:18 +00:00
PipelineUtils.scala	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
ProcessController.scala	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00
ReflectionUtils.scala	Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines.	2010-10-20 21:43:52 +00:00
Retry.scala	Emergency fix for Ryan:	2010-10-13 22:22:01 +00:00
RetryException.scala	Emergency fix for Ryan:	2010-10-13 22:22:01 +00:00
ScalaCompoundArgumentTypeDescriptor.scala	Get rid of the static cache of ArgumentTypeDescriptors by making them an integral part of the	2010-10-27 19:44:55 +00:00
ShellJob.scala	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00
SystemUtils.scala	Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline.	2010-10-14 15:58:52 +00:00
TextFormatUtils.scala	Emergency fix for Ryan:	2010-10-13 22:22:01 +00:00