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GUDMAP_RBK
RNA-seq
Commits
984d0810
Commit
984d0810
authored
3 years ago
by
Gervaise Henry
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Fix uploadExecutionRun and uploadQC CI exist
parent
d0448f31
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2 merge requests
!95
Update rna-seq.nf
,
!91
Resolve "Change the CI unit test RIDs"
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#10491
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in 9 minutes and 36 seconds
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.gitlab-ci.yml
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984d0810
...
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@@ -452,7 +452,7 @@ uploadExecutionRun:
-
echo ${dir}${derivaImg}_${derivaVar}.sif
-
ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
-
>
exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Replicate=
17-BTFJ
) &&
exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Replicate=
${ci_staging_rid_test_rep}
) &&
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
if [ "${exist}" == "[]" ]; then
...
...
@@ -479,7 +479,7 @@ uploadQC:
-
echo ${dir}${derivaImg}_${derivaVar}.sif
-
ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
-
>
exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:mRNA_QC/Replicate=
17-BTFJ
) &&
exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:mRNA_QC/Replicate=
${ci_staging_rid_test_rep}
) &&
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
if [ "${exist}" != "[]" ]; then
...
...
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