Updated the FCP, the test, and the ADPR to handle an issue with the ADPR locating the yaml generated by the FCPTest.
Does not solve the ADPR error: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5126 348d0f76-0448-11de-a6fe-93d51630548a
Moved the BamListWriter from FCP to ListWriterFunction in the Queue core.
Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s.
Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a
- Reading the refseq table from the YAML if not specified on the command line.
- Removed obsolete -bigMemQueue now that CombineVariants runs in 4g.
- Added a -mountDir /broad/software option to work around adpr automount issues.
- Merged the LSF preexec used for automount into the shell script used to execute tasks.
- Using the LSF C Library to determine when jobs are complete instead of postexec.
- Updated queue.sh to match the changes above.
- Updated the FCPTest to match the changes above.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5036 348d0f76-0448-11de-a6fe-93d51630548a
Changed the FCP.q to use an InProcessFunction work around the -runDir issue GSA-420.
Tested the FCPTest using the following dotkits and "ant clean pipelinetest -Dpipeline.run=run":
- R-2.11
- Oracle-full-client
- .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5029 348d0f76-0448-11de-a6fe-93d51630548a
R-2.10,
Oracle-full-client,
cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
This also removes the unused titv argument
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5024 348d0f76-0448-11de-a6fe-93d51630548a
.Lifted to HapMap 3.3
.Lifted to dbSNP 132 where possible.
.Added the CEU-Trio WEx(hg19) dataset
.Added some options to the pipeline
You can now use :
-dataset WEX
-dataset HiSeq
...
to choose which datasets to run through the pipeline.
You can now without BAQ and indel mask:
-noBAQ
-noMASK
Choose not to run the gold standard comparison analysis:
-skipGoldStandard
Activate the VariantEval walker analysis on the Recalibrated vcf:
-eval
The default behavior is to run exactly like it used to, so this version shouldn't change the way you used to use the pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5004 348d0f76-0448-11de-a6fe-93d51630548a
GSA-410 Local job runs now can run command lines longer than than 4096 on our linux machines.
When determining if the help text and Queue extensions need to be rebuilt, use the .class files not the .java so that GATK oneoffs are picked up correctly.
Added the most basic of all example QScripts for debugging, Hello World.
Minor updates to copy/pasted LSF code to reduce ant javadoc warnings by a third.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4970 348d0f76-0448-11de-a6fe-93d51630548a
Updated the Queue scatter/gather for read walkers to include -L unmapped on the last scatter job when intervals aren't specified, and to map it correctly when it is explicitly set.
Simplified the build.xml/ivy.xml to fix a bug reported with "ant clean dist test" where the scalac target wasn't found.
Now building all scala code at the same time, just like all java code is compiled at the same time.
Sped up the build for everyone by uncommenting a small bit of classes so that javac/scalac will not constantly launch trying to build .class files that will never compile.
Moved some source files to their expected location so that the .java/.scala -> .class is a one-to-one match, again keeping the compilers from wasting cycles.
Used <uptodate> and <touch> to skip extracting the help text and generating the GATK Queue extensions when the source files haven't been modified.
Fixed a couple errors when the <javadoc> task is run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4963 348d0f76-0448-11de-a6fe-93d51630548a
Adding the first version of the techdev pipeline (tdPipeline)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4943 348d0f76-0448-11de-a6fe-93d51630548a
+ GroupIntervals allows user-defined scattering (e.g. take an interval list file, split it into k smaller interval list files by number of lines)
+ ExpandIntervals expands the intervals, either by widening them, or allowing the definition for nearby intervals (e.g. flanks starting 1bp before and after, ending 10bp after that)
+ IntersectIntervals takes n interval lists, writes 1 interval list that is the n-way intersection of all of them
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4885 348d0f76-0448-11de-a6fe-93d51630548a
VariantEvalWalker's logger is made public, so that variant eval modules can access it through the parent object.
DesignFileGenerator comment lists how best to bind things to it, and the feature accessor is better refined to grab the genome loc. (old change)
scala changes:
convenience addAll( List[CommandLineFunction] ) added to QScript class (and thus removed from the fCPV2)
useful command line functions added to a new library package for command line functions (these are fast simple VCF command lines)
bug fixed in ProjectManagement for the class where there's only one batch to be batch-merged (not really part of the use-case, but an edge-condition that came up during pipeline testing)
first draft of a private mutations pipeline which will be elaborated in future
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4823 348d0f76-0448-11de-a6fe-93d51630548a
- 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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4816 348d0f76-0448-11de-a6fe-93d51630548a
Arguments to the full calling qscript (and indeed, any qscript that wants them) are now specified via the PipelineArgumentCollection
Libraries require a Pipeline object for instantiation -- eliminating their previous dependence on yaml files
Functions added to PipelineUtils to build out the proper Pipeline object from the PipelineArgumentCollection, which now contains
additional arguments to specify pipeline properties (name, ref, bams, dbsnp, interval list); which are mutually exclusive with
the yaml file.
Pipeline length reduced to a mere 62 lines.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4790 348d0f76-0448-11de-a6fe-93d51630548a
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
Bug fix to LiftoverVariants - no barfing at reference sites.
AlleleFrequencyComparison - local changes added to make sure parsing works properly
Added HammingDistance annotation. Mostly useless. But only mostly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4622 348d0f76-0448-11de-a6fe-93d51630548a
Updated a call to swapExt to specify the directory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4586 348d0f76-0448-11de-a6fe-93d51630548a
- Forcing user to set the temp directory via -Djava.io.tmpdir to avoid filling up /tmp.
- By default deleting job outputs tagged as intermediate.
- Defaulting pipeline to scatter count 1 (no reads deleted).
- Cleaning up temp classes even when scripting fails.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4573 348d0f76-0448-11de-a6fe-93d51630548a
When the cleaner interval scatter count is set to one explicitly setting the intrevals to Nil.
TODO: Need to add an option that lets the user choose from the command line to scatter all contigs or just those in the intervals list. For now can get relatively the same behavior by setting the interval scatter count equal to the number of contigs+1, assuming the random contigs come at the end of the sequence dictionary.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4565 348d0f76-0448-11de-a6fe-93d51630548a
Added a brute force -retry <count> option to Queue for transient errors.
Waiting up to 2 minutes for the LSF logs to appear before trying to display the errors from the logs.
Updates to the local job runner error logging when a job fails.
Refactored QGraph's settings as duplicate code was getting out of control.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4563 348d0f76-0448-11de-a6fe-93d51630548a
- More cleanup including removing the temporary classes and intermediate error files. Quieting any errors using Apache Commons IO 2.0.
- Counting the contigs during the QScript generation instead of the end user having to pass a separate contig interval list.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4539 348d0f76-0448-11de-a6fe-93d51630548a
Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator.
Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered.
Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers.
Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 348d0f76-0448-11de-a6fe-93d51630548a
Re-logging the failed jobs and the path to their log files at the end of a run.
Added a parameter -bigMemQueue for the fullCallingPipeline.q instead of hardcoding gsa (gsa was backed up and it was actually faster to run on week).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4520 348d0f76-0448-11de-a6fe-93d51630548a
Modified - SelectVariants: Hook up to VariantContextUtils to recalculate AC/AF/AN, which uses the accessor in VariantContext to do this. Somehow sites that were selected down to hom-ref genotypes only wound up getting positive AC.
**IMPORTANT** I kind of need input here. The header of a file used for an integration test specifies AC as being an integer. Recalculating it casts it into an integer list (which it should be, as it allows for alternate alleles). However this appears to clash with what the jexl expression is looking for? For now, the integration test itself needed to be changed -- it's unclear what to do when the header specifies AC of being one class, but recalculating it casts to another class, and I'm not sure what to do.
I'm committing my omni_qc pipeline because I'm almost certain 2 months down the road I'm going to wonder what the heck I did to generate my results.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4511 348d0f76-0448-11de-a6fe-93d51630548a
Updated pipeline output structure to current recommendations by Corin.
Directories are now automatically before the function runs.
Fixed several bugs with scatter gather binding when the script author needs to change the directories.
Fixed bug with tracking of log files for CloneFunctions.
More error handling and logging of exceptions (good test environment while LSF was down this early AM!)
Removed cleanup utility for scatter gather. SG Output structure has changed significantly. Will need to discuss and find a better approach for Queue programatically deleting files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4504 348d0f76-0448-11de-a6fe-93d51630548a
carneiro
rpoplin
fromer
kshakir
corin
ebanks
delangel
depristo
chartl
kiran
hanna