Added targets to build.xml to effectively 'mvn install' packaged GATK/Queue from ant.
TODO: Versions during 'mvn install' are hardcoded at 0.0.1 until a better versioning scheme that works with maven dependencies has been identified.
The NullPointerException we were seeing when trying to run with contracts enabled was being caused
by an outdated version of the asm library.
To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant.
Also did some minor unrelated cleanup in build.xml
Temporarily disabled contracts in integrationtests until we can find the cause
of the new error that's cropping up for Ryan.
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only download that test configuration when running unit/integration tests.
This means that the build will (hopefully) never break because it can't
fetch a file that isn't required for the GATK to run.
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though sonatype is back up). This will tide us over until I figure out how
to add caliper to test configuration, so that it's only swapped in when we
actually run our unit / performance tests.
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but I'm still not sure that GC is a good long-term solution.
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- bsub command line is no longer fully printed out.
- extraBsubArgs hack is now a callback function updateJobRun.
Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q.
Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits.
Updated VE packages that live in oneoffs to compile to oneoffs.
Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac.
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Shell invoking scripts so that even really long shell scripts make it through LSF.
Using the truncated (up to 1000 characters) of the command line for the job name for use with bjobs.
Switched the default from re-running everything to re-running only files that need to be regenerated. --skip_up_to_date replaced with --start_clean for those who want to regenerate everything.
Updated logging to let users know when the scatter gather generator is running, which still takes a while but is orders of magnatudes faster for large lists of functions. (40s for a 100 function graph exploding to a 2500 function graph)
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removed the auto-deletion of the reflections jar, and removed the very old OmniPlan document we had checked-in.
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Changes to StingUtils command line for use in Queue, replacing Queue's use of property files.
Updates to walkers used in existing QScripts to add @Input/@Output.
RMD used in @Required/@Allows now has a new default equal to "any" type.
New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions.
Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.)
Removed dependency on BroadCore by porting LSF job submitter to scala.
Ivy now pulls down module dependencies from maven.
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inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.
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kshakir
Matt Hanna
David Roazen
hanna
kshakir
aaron