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GUDMAP_RBK
RNA-seq
Commits
686d27d4
Commit
686d27d4
authored
4 years ago
by
Gervaise Henry
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Use the correct docker container for upload processed files ci unit
parent
9da15a83
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!58
Develop
,
!53
Resolve "process_derivaUpload"
Pipeline
#8613
canceled with stages
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686d27d4
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@@ -355,7 +355,7 @@ uploadProcessedFile:
-
>
exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) &&
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1}
&&
cookie=${cookie:11:-1}
if [ "${exist}" != "[]" ]; then
rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//')
for rid in ${rids}; do
...
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@@ -364,10 +364,10 @@ uploadProcessedFile:
done
echo all old processed file RIDs deleted
fi
-
singularity run 'docker://
bicf/
gudmaprbk
filexfer:2.0.1_indev
' deriva-upload-cli --catalog 2 --token ${cookie} staging.gudmap.org ./deriva
-
singularity run 'docker://gudmaprbk
/deriva1.3:1.0.0
' deriva-upload-cli --catalog 2 --token ${cookie} staging.gudmap.org ./deriva
-
echo test processed file uploaded
-
mkdir test
-
singularity run 'docker://
bicf/
gudmaprbk
filexfer:2.0.1_indev
' bdbag test --archiver zip
-
singularity run 'docker://gudmaprbk
/deriva1.3:1.0.0
' bdbag test --archiver zip
-
echo test output bag created
-
pytest -m outputBag
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