changeset 1:3a37867409fe draft

Uploaded
author elixir-it
date Thu, 15 Nov 2018 15:57:12 -0500
parents 6d8aa1176a94
children 5058867ac48f
files mv_untar_gatk.sh tool-data/covacs_gatk_indexes.loc.sample
diffstat 2 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- 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
+
--- 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