Commit 2221fa53 authored by Peter van 't Hof's avatar Peter van 't Hof

Merge branch 'fix-BIOPET-484' into 'develop'

Changes to the documentation for developers

BIOPET-484 Issue in JIRA

See merge request !488
parents 0efd042b b5f0c35a
......@@ -141,7 +141,7 @@ object WriteDependencies extends Logging with Configurable {
val jobsDeps = jobs.map(x => x._1 -> (x._2("depends_on_jobs") match {
case l: List[_] => l.map(_.toString)
case _ => throw new IllegalStateException("Value 'depends_on_jobs' is not a list")
case _ => throw new IllegalStateException("Value 'depends_on_jobs' is not a list")
}))
val jobsWriter = new PrintWriter(new File(outputDir, s"$prefix.jobs.json"))
jobsWriter.println(ConfigUtils.mapToJson(jobsDeps).spaces2)
......
......@@ -59,10 +59,10 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
for ((_, l) <- qscript.summarizables; s <- l) s match {
case f: QFunction => try {
deps :+= f.firstOutput
} catch {
} catch {
case e: NullPointerException => logger.warn("Queue values are not init")
}
case _ =>
case _ =>
}
jobOutputFile = new File(out.getParentFile, ".%s.%s.out".format(out.getName, analysisName))
......
......@@ -16,17 +16,17 @@ Make sure both tools are installed in your local maven repository. To do this on
```bash
# Replace 'mvn' with the location of you maven executable or put it in your PATH with the export command.
git clone https://github.com/broadgsa/gatk-protected
cd gatk-protected
git checkout 3.4
# The GATK version is bound to a version of Biopet. Biopet 0.5.0 uses Gatk 3.4
git clone https://github.com/broadgsa/gatk
cd gatk
git checkout 3.6
# The GATK version is bound to a version of Biopet. Biopet 0.7.0 uses Gatk 3.6
mvn clean install
cd ..
git clone https://github.com/biopet/biopet.git
cd biopet
git checkout 0.5.0
git checkout 0.7.0
mvn -DskipTests=true clean install
```
......
......@@ -19,11 +19,11 @@ import java.util.Date
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie, Bowtie2}
import nl.lumc.sasc.biopet.extensions.bwa.{BwaAln, BwaMem, BwaSampe, BwaSamse}
import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie, Bowtie2 }
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import nl.lumc.sasc.biopet.extensions.picard.{AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam}
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
......
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