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

Fix syntax.

parent c4859ad3
...@@ -44,31 +44,32 @@ main(){ ...@@ -44,31 +44,32 @@ main(){
# query GUDMAP/RBK for study RID # 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 > $rid\_studyRID.json echo "curl --location --request GET 'https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Replicate/Study_RID="${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 # cleanup study RID files
rm $rid\_studyRID.json rm $rid\_studyRID.json
# make dir for study # make dir for study
mkdir $out/$rid mkdir $out/$rid
mv $rid\_studyRID.csv $out/$rid mv $rid\_studyRID.csv $out/$rid
cd $out/$rid cd $out/$rid
# download version of RNA-seq pipelne # download version of RNA-seq pipelne
existed_in_remote=$( git ls-remote --tags git@git.biohpc.swmed.edu:gudmap_rbk/rna-seq.git ${tag}) existed_in_remote=$( git ls-remote --tags git@git.biohpc.swmed.edu:gudmap_rbk/rna-seq.git ${tag})
if [[ -z ${existed_in_remote} ]]; then if [[ -z ${existed_in_remote} ]]; then
echo "The tag ${tag} doesn't exist." echo "The tag ${tag} doesn't exist."
exit 1 exit 1
fi 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 # run pipeline on replicate RIDs in parallel
cd rna-seq 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 ${email} -with-report ./output/{}_report.html -with-timeline ./output/{}_timeline.html
} }
main "$@" main "$@"
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