Commit 88d51c42 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding all Jars

parent 2c2e3865
package nl.lumc.sasc.biopet.tools.vcfstats package nl.lumc.sasc.biopet.tools.vcfstats
import java.io.{File, PrintWriter} import java.io.{File, PrintWriter}
import java.net.URLClassLoader
import htsjdk.variant.vcf.VCFFileReader import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats._ import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats._
...@@ -124,6 +125,7 @@ object VcfStatsSpark extends ToolCommand { ...@@ -124,6 +125,7 @@ object VcfStatsSpark extends ToolCommand {
val conf = new SparkConf() val conf = new SparkConf()
.setAppName(this.getClass.getSimpleName) .setAppName(this.getClass.getSimpleName)
.setMaster(cmdArgs.sparkMaster.getOrElse(s"local[${cmdArgs.localThreads}]")) .setMaster(cmdArgs.sparkMaster.getOrElse(s"local[${cmdArgs.localThreads}]"))
.setJars(ClassLoader.getSystemClassLoader.asInstanceOf[URLClassLoader].getURLs.map(_.getFile))
val sc = new SparkContext(conf) val sc = new SparkContext(conf)
logger.info("Spark context is up") logger.info("Spark context is up")
...@@ -183,7 +185,6 @@ object VcfStatsSpark extends ToolCommand { ...@@ -183,7 +185,6 @@ object VcfStatsSpark extends ToolCommand {
cmdArgs.outputDir + "/sample_compare/allele_overlap", cmdArgs.outputDir + "/sample_compare/allele_overlap",
samples) samples)
Thread.sleep(1000000)
sc.stop sc.stop
logger.info("Done") logger.info("Done")
} }
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment