diff mutect2.xml @ 10:e3662508ee26 draft

Uploaded

--- 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