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GUDMAP_RBK
data_hub_scripts
Commits
55615bed
Commit
55615bed
authored
Jan 11, 2021
by
Venkat Malladi
Browse files
Add out dir.
parent
db5270b5
Changes
1
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Inline
Side-by-side
scripts/split_study.sh
View file @
55615bed
...
...
@@ -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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