Commit 55615bed authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Add out dir.

parent db5270b5
......@@ -12,7 +12,8 @@ usage() {
echo "-h --Help documentation for $script_name"
echo "-r --Study_RID."
echo "-t --Tag of pipelne"
echo "Example: $script_name -r 16-1ZP0 -t 0.1.0"
echo "-o --Path to output directory"
echo "Example: $script_name -r 16-1ZP0 -t 0.1.0 -o '/path/to/output/dir/'"
exit 1
}
......@@ -25,11 +26,12 @@ main(){
# Parsing options
OPTIND=1 # Reset OPTIND
while getopts :r:t:h opt
while getopts :r:t:0:h opt
do
case $opt in
r) rid=$OPTARG;;
t) tag=$OPTARG;;
o) out=$OPTARG;;
h) usage;;
esac
done
......@@ -37,7 +39,7 @@ main(){
shift $(($OPTIND -1))
# Check for mandatory options
if [[ -z $rid ]] || [[ -z $tag ]]; then
if [[ -z $rid ]] || [[ -z $tag ]] || [[ -z $out ]]; then
usage
fi
......@@ -52,9 +54,9 @@ main(){
rm $rid\_studyRID.json
# make dir for study
mkdir $rid
mv $rid\_studyRID.csv $rid
cd $rid
mkdir $out/$rid
mv $rid\_studyRID.csv $out/$rid
cd $out/$rid
# download version of RNA-seq pipelne
existed_in_remote=$( git ls-remote --tags git@git.biohpc.swmed.edu:gudmap_rbk/rna-seq.git ${tag})
......
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