Commit db5270b5 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Update split study.

parent ece65739
......@@ -4,18 +4,71 @@
#SBATCH --job-name GUDMAP-RBK_Study
#SBATCH -t 7-0:0:0
# query GUDMAP/RBK for study RID
echo "curl --location --request GET 'https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Replicate/Study_RID="${1}"'" | bash > $1_studyRID.json
# extract replicate RIDs
module load python/3.6.4-anaconda
python3 ./workflow/scripts/split_study.py -s $1
script_name="split_study.sh"
# run pipeline on replicate RIDs in parallel
module load nextflow/20.01.0
module load singularity/3.5.3
while read repRID; do echo ${repRID}; sleep 30; done < "$1_studyRID.csv" | xargs -P 5 -I {} nextflow -q run workflow/rna-seq.nf --repRID {} --source production --deriva /project/BICF/BICF_Core/shared/gudmap/test_data/auth/credential.json --bdbag /project/BICF/BICF_Core/shared/gudmap/test_data/auth/cookies.txt --dev false --upload true --email gervaise.henry@utsouthwestern.edu -with-report ./output/{}_report.html -with-timeline ./output/{}_timeline.html
#Help function
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"
exit 1
}
# cleanup study RID files
rm $1_studyRID.json
#rm $1_studyRID.csv
main(){
# Load required modules
module load python/3.6.4-anaconda
module load nextflow/20.01.0
module load singularity/3.5.3
# Parsing options
OPTIND=1 # Reset OPTIND
while getopts :r:t:h opt
do
case $opt in
r) rid=$OPTARG;;
t) tag=$OPTARG;;
h) usage;;
esac
done
shift $(($OPTIND -1))
# Check for mandatory options
if [[ -z $rid ]] || [[ -z $tag ]]; then
usage
fi
# query GUDMAP/RBK for study RID
echo "curl --location --request GET 'https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Replicate/Study_RID="${rid}"'" | bash > $rid\_studyRID.json
# extract replicate RIDs
python3 ./scripts/split_study.py -s $rid
# cleanup study RID files
rm $rid\_studyRID.json
# make dir for study
mkdir $rid
mv $rid\_studyRID.csv $rid
cd $rid
# download version of RNA-seq pipelne
existed_in_remote=$( git ls-remote --tags git@git.biohpc.swmed.edu:gudmap_rbk/rna-seq.git ${tag})
if [[ -z ${existed_in_remote} ]]; then
echo "The tag ${tag} doesn't exist."
exit 1
fi
git clone -b $tag --depth 1 git@git.biohpc.swmed.edu:gudmap_rbk/rna-seq.git
cd rna-seq
# run pipeline on replicate RIDs in parallel
while read repRID; do echo ${repRID}; sleep 30; done < "../${rid}_studyRID.csv" | xargs -P 5 -I {} nextflow -q run workflow/rna-seq.nf --repRID {} --source production --deriva /project/BICF/BICF_Core/shared/gudmap/test_data/auth/credential.json --bdbag /project/BICF/BICF_Core/shared/gudmap/test_data/auth/cookies.txt --dev false --upload true --email gervaise.henry@utsouthwestern.edu -with-report ./output/{}_report.html -with-timeline ./output/{}_timeline.html
}
main "$@"
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