# HG changeset patch
# User elixir-it
# Date 1542315432 18000
# Node ID 3a37867409fe6f680f50fd34584999ab2d5b0958
# Parent  6d8aa1176a94e29f271fef020f617974789d3465
Uploaded

diff -r 6d8aa1176a94 -r 3a37867409fe mv_untar_gatk.sh
--- a/mv_untar_gatk.sh	Fri Nov 09 06:03:28 2018 -0500
+++ b/mv_untar_gatk.sh	Thu Nov 15 15:57:12 2018 -0500
@@ -2,8 +2,9 @@
 #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 -zxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.gz -C $CONDA_PREFIX/../../ 
-	
+        tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar
+
 else
-	echo GATK is present
+        echo GATK is present
 fi
+
diff -r 6d8aa1176a94 -r 3a37867409fe tool-data/covacs_gatk_indexes.loc.sample
--- a/tool-data/covacs_gatk_indexes.loc.sample	Fri Nov 09 06:03:28 2018 -0500
+++ b/tool-data/covacs_gatk_indexes.loc.sample	Thu Nov 15 15:57:12 2018 -0500
@@ -32,5 +32,5 @@
 #is the value stored in the workflow for that parameter. That is why the
 #hg19 entry above looks odd. New genomes can be better-looking.
 #
-hg38	hg38	hg38_GDC	/export/gatkhg38pl/GRCh38.d1.vd1.fa
-hg19	hg19	hg19	/export/gatk_hg19_index_bundle/ucsc.hg19.fasta
+#hg38	hg38	hg38_GDC	/export/gatkhg38pl/GRCh38.d1.vd1.fa
+#hg19	hg19	hg19	/export/gatk_hg19_index_bundle/ucsc.hg19.fasta