Commit ea5087f8 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Fix syntax.

parent c4859ad3
......@@ -44,31 +44,32 @@ main(){
# 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
# extract replicate RIDs
python3 ./scripts/split_study.py -s $rid
python3 ./scripts/split_study.py -s $rid
# cleanup study RID files
rm $rid\_studyRID.json
# cleanup study RID files
rm $rid\_studyRID.json
# make dir for study
mkdir $out/$rid
mv $rid\_studyRID.csv $out/$rid
cd $out/$rid
# make dir for study
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 ${tag})
# download version of RNA-seq pipelne
existed_in_remote=$( 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
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
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 ${email} -with-report ./output/{}_report.html -with-timeline ./output/{}_timeline.html
# 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 ${email} -with-report ./output/{}_report.html -with-timeline ./output/{}_timeline.html
}
main "$@"
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