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Pipeline tests will only start from scratch after "ant clean", making it faster to debug downstream issues when re-running "ant pipelinetest -Dpipeline.run=run". 

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
This commit is contained in:
kshakir 2011-01-29 19:44:03 +00:00
parent b0a3c70f90
commit 23578b7402
4 changed files with 18 additions and 14 deletions
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5
R/DataProcessingReport/GetTearsheetStats.R
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@ -16,6 +16,7 @@ suppressMessages(library(ROracle));
cmdargs = gsa.getargs( cmdargs = gsa.getargs(
list( list(
yaml = list(value=NA, doc="pipeline YAML file"),
bamlist = list(value=NA, doc="list of BAM files"), bamlist = list(value=NA, doc="list of BAM files"),
evalroot = list(value=NA, doc="VariantEval root"), evalroot = list(value=NA, doc="VariantEval root"),
tearout = list(value=NA, doc="Output path for tearsheet PDF")#, tearout = list(value=NA, doc="Output path for tearsheet PDF")#,
@ -26,8 +27,8 @@ cmdargs = gsa.getargs(
bamlist = scan(cmdargs$bamlist, "character"); bamlist = scan(cmdargs$bamlist, "character");
print(paste("grep SQUID ", sub("cleaned.BamFiles.list", "yaml",cmdargs$bamlist) , ' |grep "C..." -o', sep="")) print(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o', sep=""))
squids <- system(paste("grep SQUID ", sub("cleaned.BamFiles.list", "yaml",cmdargs$bamlist) , ' |grep "C..." -o', sep=""), intern=TRUE) squids <- system(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o', sep=""), intern=TRUE)
fclanes = c(); fclanes = c();
for (bam in bamlist) { for (bam in bamlist) {
bamheader = system(paste("samtools view -H", bam), intern=TRUE); bamheader = system(paste("samtools view -H", bam), intern=TRUE);

15
scala/qscript/playground/fullCallingPipeline.q
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@ -385,20 +385,23 @@ class fullCallingPipeline extends QScript {
// 6. Run the ADPR and make pretty stuff // 6. Run the ADPR and make pretty stuff
class rCommand extends CommandLineFunction{ class rCommand extends CommandLineFunction{
@Argument(doc="R script") @Input(doc="R script")
var script: File = _ var script: File = _
@Argument(doc="list of bams") @Input(doc="pipeline yaml")
var bamlist: File =_ var yaml: File = _
@Input(doc="list of bams")
var bamlist: File =_
@Input(doc="Eval files root") @Input(doc="Eval files root")
var evalroot: File =_ var evalroot: File =_
@Output(doc="tearsheet loc") @Output(doc="tearsheet loc")
var tearsheet: File =_ var tearsheet: File =_
def commandLine = "Rscript %s -bamlist %s -evalroot %s -tearout %s" def commandLine = "Rscript %s -yaml %s -bamlist %s -evalroot %s -tearout %s"
.format(script, bamlist, evalroot, tearsheet) .format(script, yaml, bamlist, evalroot, tearsheet)
} }
val adpr = new rCommand val adpr = new rCommand
adpr.bamlist = listOfBams adpr.bamlist = listOfBams
adpr.yaml = qscript.yamlFile.getAbsoluteFile
adpr.script = tearScript adpr.script = tearScript
adpr.evalroot = eval.reportLocation adpr.evalroot = eval.reportLocation
adpr.jobOutputFile = new File(".queue/logs/SNPCalling/adpr.out") adpr.jobOutputFile = new File(".queue/logs/SNPCalling/adpr.out")

2
scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
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@ -120,7 +120,7 @@ object PipelineTest {
// add the logging level to each of the integration test commands // add the logging level to each of the integration test commands
command = Utils.appendArray(command, "-bsub", "-l", "WARN", "-startFromScratch", "-tempDir", tempDir(name), "-runDir", runDir(name)) command = Utils.appendArray(command, "-bsub", "-l", "WARN", "-tempDir", tempDir(name), "-runDir", runDir(name))
if (jobQueue == null) if (jobQueue == null)
command = Utils.appendArray(command, "-jobQueue", "hour") command = Utils.appendArray(command, "-jobQueue", "hour")

10
scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala
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@ -95,7 +95,7 @@ class FullCallingPipelineTest {
def testFullCallingPipeline(dataset: PipelineDataset) = { def testFullCallingPipeline(dataset: PipelineDataset) = {
val projectName = dataset.pipeline.getProject.getName val projectName = dataset.pipeline.getProject.getName
val testName = "fullCallingPipeline-" + projectName val testName = "fullCallingPipeline-" + projectName
val yamlFile = writeTempYaml(dataset.pipeline) val yamlFile = writeYaml(testName, dataset.pipeline)
var cleanType = "cleaned" var cleanType = "cleaned"
// Run the pipeline with the expected inputs. // Run the pipeline with the expected inputs.
@ -134,9 +134,9 @@ class FullCallingPipelineTest {
override def toString = pipeline.getProject.getName override def toString = pipeline.getProject.getName
} }
private def writeTempYaml(pipeline: Pipeline) = { private def writeYaml(testName: String, pipeline: Pipeline) = {
val tempFile = BaseTest.createTempFile(pipeline.getProject.getName + "-", ".yaml") val yamlFile = new File(PipelineTest.runDir(testName), pipeline.getProject.getName + ".yaml")
YamlUtils.dump(pipeline, tempFile) YamlUtils.dump(pipeline, yamlFile)
tempFile yamlFile
} }
} }