# HG changeset patch
# User elixir-it
# Date 1542315291 18000
# Node ID 48dc4c9bc4973fd60772638d5ac8051200d09399
# Parent  c785cec34cdcfaabe379e94457acb3259ff79bd9
Uploaded

diff -r c785cec34cdc -r 48dc4c9bc497 mv_untar_gatk.sh
--- a/mv_untar_gatk.sh	Fri Nov 09 05:27:39 2018 -0500
+++ b/mv_untar_gatk.sh	Thu Nov 15 15:54:51 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 c785cec34cdc -r 48dc4c9bc497 tool-data/covacs_bed.loc.sample
--- a/tool-data/covacs_bed.loc.sample	Fri Nov 09 05:27:39 2018 -0500
+++ b/tool-data/covacs_bed.loc.sample	Thu Nov 15 15:54:51 2018 -0500
@@ -13,5 +13,5 @@
 #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.
 #
-hg19	hg19	hg19-padded	/export/BED/S07084713_Padded.bed
-hgbed	hg19	hg19-bed-test	/export/BED/chr22.bed
+#hg19	hg19	hg19-padded	/export/BED/S07084713_Padded.bed
+#hgbed	hg19	hg19-bed-test	/export/BED/chr22.bed
diff -r c785cec34cdc -r 48dc4c9bc497 tool-data/covacs_gatk_indexes.loc.sample
--- a/tool-data/covacs_gatk_indexes.loc.sample	Fri Nov 09 05:27:39 2018 -0500
+++ b/tool-data/covacs_gatk_indexes.loc.sample	Thu Nov 15 15:54:51 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