6d22f4f737
Bringing latest performance updates from the GATK to CMI
2012-12-05 21:40:03 -05:00
61bde6210b
Restored RemoteFile push and pull in base QScript.
2012-12-04 12:34:07 -05:00
97d29f203e
Add walltime changes to LSF
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- Check whether the specified attribute is available
- Add pipeline test (disabled due to missing attribute)
2012-11-29 15:23:37 -05:00
daf6269b65
Setting the walltime
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Signed-off-by: Joel Thibault <thibault@broadinstitute.org>
2012-11-29 15:23:36 -05:00
a6c1fcd151
Removed default use of @Output syntax.
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If compile completes for QScripts, sending runtime errors during execute.
2012-11-29 13:40:36 -05:00
a8c7edca05
Fixed fragment handling in DepthOfCoverage
2012-11-21 16:01:10 -05:00
c8be7c3102
Keep SNPs and indels separately for batch merging; Add options to DepthOfCoverage to count fragments (to not double-count overlapping reads of same fragment); DepthOfCoverage should now support ReducedReads; Replace recusrion with loop in DoC/package.scala (for lists longer than 5000 elements)
2012-11-21 15:56:53 -05:00
9111966261
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-11-20 12:19:58 -05:00
843384e435
Rename hg19 files in bundle to b37 since that's what they are
2012-11-14 11:47:09 -05:00
e35fd1c717
Merging CMI-0.5.0 and GATK-2.2 together.
2012-11-14 10:42:03 -05:00
6d59dd3455
Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass.
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Removed some generics from PluginManager for now until able to figure out syntax for requesting explicit subclass.
QStatusMessenger uses a slightly more primitive Map[String, Seq[RemoteFile]] instead of Map[ArgumentSource, Seq[RemoteFile]].
Added an QCommandPlugin.initScript utility method for handling specialized script types.
2012-11-14 10:33:20 -05:00
73157ae3d3
Allow each pipeline test the max of 10 hours to run
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The runtime of these tests is extremely variable -- sometimes they will complete almost instantly,
other times they will wait in an LSF queue for 5-10+ hours. Minimize timeout errors by setting the
timeout for these tests to the maximum of 10 hours.
2012-11-02 12:40:56 -04:00
51a9ce28e1
Merge remote-tracking branch 'unstable/master' into develop
2012-10-31 10:29:48 -04:00
eccb76c304
Only run UG in the bundle for chr20
2012-10-30 15:09:46 -04:00
8a402024c2
Updating bundle script to handle new naming convention of CEU trio best practices callset
2012-10-30 09:11:56 -04:00
5ee2feb2a3
updating pipeline test md5s
2012-10-29 18:53:27 -04:00
9af4b34fd8
Changed @Input to @Argument for non-File types
2012-10-26 01:21:05 -04:00
0fe36b1c72
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-10-25 16:18:57 -04:00
cde4f037d3
Begin moving XHMM scripts to public
2012-10-25 16:18:25 -04:00
dde3060bb8
add the CEUtrio best practices results (UG + PBT) to the bundle
2012-10-25 15:36:17 -04:00
8dfa24df7b
Sending a version of per job status messages.
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In addition to outputs, inputs are passed to QStatusMessenger.done()
CloneFunction.cloneIndex has a new CloneFunction.cloneCount companion useful for display purposes.
2012-10-23 15:55:47 -04:00
5fac5bf12e
Fixed issues with Queue packaging of Picard QC classes: separate jar's are needed fromPicard. User needs to specify the -picardBase argument to point to input path for jars.
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> Also, reenable joint cleaning as now it works.
> DEV-125 #resolve
> DEV-90 #resolve
2012-10-23 14:08:31 -04:00
0cce1ae8b2
When gathering VCFs, using CombineVariants from the current classpath, and not the GATK used to run the command. This was a concern for external modules that bundled the engine but not CombineVariants.
2012-10-23 12:44:06 -04:00
c210b7cde4
Merge GATK repo into CMI-GATK
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Bringing in the following relevant changes:
* Fixes the indel realigner N-Way out null pointer exception DEV-10
* Optimizations to ReduceReads that bring the run time to 1/3rd.
Conflicts:
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
DEV-10 #resolve #time 2m
2012-10-23 10:59:11 -04:00
7860ff7981
a) Resolve [#DEV-56] - test data with indels in new directory private/testdata/CMITestData/. b) Skeleton (not yet working) of fastq-BAM unit test, c) misc bug fixes for QC functions to work (not done yet)
2012-10-22 19:59:15 -04:00
fd59e7d5f6
Better error message when generic types are erased from scala collections.
2012-10-22 16:27:31 -04:00
2ef456d51a
Added explicit @ClassType annotations to @Argument for Option[Int] or Option[Double] since scala seems to change the reflected type to Option[Object] on some systems.
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Changed ReflectionUtils.getGenericTypes' order of looking for @ClassType since the primitive generic wasn't completely erased, only changed to Object which is incorrect.
More fixes to @Arguments labeled as java.io.File via incorrect @Input annotation.
Put in a default undocumented implementation of @Argument doc() to match the one added to @Input.
2012-10-19 13:20:29 -04:00
4f768e2f58
redo QC picard parts
2012-10-19 12:25:46 -04:00
403654d40a
Fixed null checkes in ArgumentTypeDescriptor due to ArgumentMatchValue updates.
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Fixed @Arguments such as scatter count that were labeled as java.io.File via incorrect @Input annotation.
2012-10-18 16:57:15 -04:00
55ac4ba70b
Added another utility that can convert to RemoteFiles.
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QScripts will now generate remote versions of files if the caller has not already passed in remote versions (or the QScript replaces the passed in remote references... not good)
Instead of having yet another plugin, combined QStatusMessenger and RemoteFileConverter under general QCommandPlugin trait.
2012-10-17 20:00:03 -04:00
0196dbeaca
Added more logging to push/pull of RemoteFiles.
2012-10-17 09:52:17 -04:00
f93b279151
Moved the class field caching from QScript to a ClassFieldCache utility.
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Using ClassFieldCache to pull values from QScript for passing to done() method of QStatusMessenger.
2012-10-16 18:49:31 -04:00
c4ee31075c
Fixed package error and a few deprecated scala warnings.
2012-10-15 15:29:40 -04:00
213cc00abe
Refactored argument matching to support other plugins in addition to file lists.
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Added plugin support for sending Queue status messages.
Argument parsing can store subclasses of java.io.File, for example RemoteFile.
2012-10-15 15:10:45 -04:00
dad7ca281e
upgraded mutation caller with VCF output
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raw indel calls (non filtered,non vcf)
2012-10-15 13:49:08 -04:00
22b79fb4dd
Resolve [DEV-7]: add single-sample VCF calling at end of FASTQ-BAM pipeline. Initial steps of [DEV-4]: queue extensions for Picard QC metrics
2012-10-15 13:49:08 -04:00
658f355171
initial cancer pipeline with mutations and partial indel support
2012-10-15 13:49:07 -04:00
322ea1262c
First implementation of a generic 'bundled' Data Processing Pipeline for germline and cancer.
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not ready for prime time yet!
2012-10-15 13:49:06 -04:00
f1fb51b222
Reverting the DPP to the original version, going to create a new simplified version for CMI in private.
2012-10-15 13:49:06 -04:00
429c96e723
Generic input file name recognition (still need to implement support to FastQ, but it now can at least accept it)
2012-10-15 13:49:06 -04:00
f66284658d
RetryMemoryLimit now works with Scatter/Gather.
2012-10-09 21:51:03 -04:00
e9b9e2318c
Fixed SortSam bug, for .done file
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The *.bai.done file for the .bai file was written in the run directory instead of in the specified output directory.
Changing getName() to getAbsolutePath() fixes this.
Signed-off-by: Joel Thibault <thibault@broadinstitute.org>
2012-10-09 16:25:18 -04:00
9a8f53e76c
Probably the GATK's most seen typo in the world
2012-10-02 13:34:37 -04:00
3f44b3e019
Update DataProcessingPipelineTest MD5s
2012-09-24 15:38:07 -04:00
277ba94c7b
Update from dbsnp135 to dbsnp137.
2012-08-31 14:06:29 -04:00
5ea7cd6dcc
Updating resource bundle: no reason to include both genotype and sites files for Omni and HM3, sites are enough. Also, don't include duplicate entry for the Mills indels.
2012-08-31 14:01:54 -04:00
2d1ea7124b
One less Queue command line requirement: -tempDir now defaults to .queue/tmp.
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Also moved queueScatterGather to .queue/scatterGather.
2012-08-27 12:04:50 -04:00
9eec33ec3b
Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running
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-- Queue will incrementally now write out its jobReport.txt file whenever jobs finish running (FAIL or DONE)
-- This makes it far easier to track what's going on, or to analyze incrementally performance results coming out of Queue
-- Generally cleaned up the QJobsReporting code, creating a new clean class QJobsReporter that holds all of the information on what to do log and where to put into, which was previously scattered in QCommandLine and QJobReport
2012-08-21 14:44:18 -04:00
3514fb6e66
Changed the default memory limit from none to 2GB upon suggestions from delangel, carneiro, and depristo.
2012-08-20 21:41:13 -04:00
67ebd65512
Bugfix for potential SEGFAULT with JNA getting execution hosts for LSF with multiple hosts
2012-08-17 11:49:01 -04:00
Mauricio Carneiro
kshakir
Joel Thibault
Johan Dahlberg
Menachem Fromer
Eric Banks
David Roazen
Guillermo del Angel
Ryan Poplin
Ami Levy Moonshine
Kristian Cibulskis
Mark DePristo