# HG changeset patch
# User elixir-it
# Date 1569184271 14400
# Node ID e3662508ee26852b4f3d2b97fedddf6a6532bcfb
# Parent  a517190d2b3d1a70cd8b1accad7c5bcdc43ce6e8
Uploaded

diff -r a517190d2b3d -r e3662508ee26 mutect2.xml
--- a/mutect2.xml	Sat Sep 21 13:21:54 2019 -0400
+++ b/mutect2.xml	Sun Sep 22 16:31:11 2019 -0400
@@ -41,10 +41,11 @@
       java -jar \$CONDA_PREFIX/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log &&
       #end if
 
-      ##TODO gatk-register take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it
-      ##and move the .jar file to \$CONDA_PREFIX/opt/gatk-3.8/ then the mutect2 command is runned
-      gatk3-register \$_CONDA_DIR/../GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 2>$log ;
-      java -jar \$CONDA_PREFIX/opt/gatk-3.8/GenomeAnalysisTK.jar -nct 4  -T MuTect2 -I:tumor tumor.bam  -I:normal normal.bam  -o $output
+      ##TODO gatk mv_untar_gatk take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it
+      ##and move  .jar and  command is runned
+      sh $__tool_directory__/mv_untar_gatk.sh &&
+
+      java -jar \$CONDA_PREFIX/../../GenomeAnalysisTK.jar -nct 4  -T MuTect2 -I:tumor tumor.bam  -I:normal normal.bam  -o $output
       #if $reference_source.reference_source_selector == "history"
       -R genome.fa
       #end if
diff -r a517190d2b3d -r e3662508ee26 mv_untar_gatk.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mv_untar_gatk.sh	Sun Sep 22 16:31:11 2019 -0400
@@ -0,0 +1,10 @@
+#!/bin/bash
+#if the .jar file is not present in the conda_prefix the script search the tar.gz in the conda_prefix of the vm
+#and untar the archive
+if [[ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ]] ; then
+        tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar
+
+else
+        echo GATK is present
+fi
+