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GUDMAP_RBK
data_hub_scripts
Commits
5ec91353
Commit
5ec91353
authored
Feb 01, 2021
by
Venkat Malladi
Browse files
Changed to dev server.
parent
7e8242c8
Changes
1
Show whitespace changes
Inline
Side-by-side
scripts/split_study.sh
View file @
5ec91353
...
...
@@ -42,7 +42,7 @@ main(){
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
echo
"curl --location --request GET 'https://
dev
.gudmap.org/ermrest/catalog/2/entity/RNASeq:Replicate/Study_RID="
${
rid
}
"'"
| bash
>
$rid
\_
studyRID.json
# extract replicate RIDs
...
...
@@ -68,7 +68,7 @@ main(){
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
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
dev
--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
}
...
...
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