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GUDMAP_RBK
data_hub_scripts
Commits
ea5087f8
Commit
ea5087f8
authored
Jan 12, 2021
by
Venkat Malladi
Browse files
Fix syntax.
parent
c4859ad3
Changes
1
Hide whitespace changes
Inline
Side-by-side
scripts/split_study.sh
View file @
ea5087f8
...
...
@@ -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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