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Commit 8e14eb0b authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add closing quote for ref ci

parent ff85155f
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2 merge requests!58Develop,!53Resolve "process_derivaUpload"
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.gitlab-ci.yml
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...@@ -458,7 +458,7 @@ human_dev: ...@@ -458,7 +458,7 @@ human_dev:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1) - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2) - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3) - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}) - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version= - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}'))
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL) - refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
...@@ -483,7 +483,7 @@ mouse_dev: ...@@ -483,7 +483,7 @@ mouse_dev:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1) - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2) - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3) - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}) - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version= - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}'))
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL) - refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
...@@ -508,7 +508,7 @@ human_staging: ...@@ -508,7 +508,7 @@ human_staging:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1) - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2) - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3) - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}) - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version= - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}'))
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL) - refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
...@@ -534,7 +534,7 @@ mouse_staging: ...@@ -534,7 +534,7 @@ mouse_staging:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1) - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2) - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3) - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}) - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version= - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}'))
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL) - refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
...@@ -559,7 +559,7 @@ human_prod: ...@@ -559,7 +559,7 @@ human_prod:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1) - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2) - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3) - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}) - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version= - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}'))
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL) - refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
...@@ -585,7 +585,7 @@ mouse_prod: ...@@ -585,7 +585,7 @@ mouse_prod:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1) - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2) - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3) - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}) - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version= - query=$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${GRCv}.${GRCp}/Annotation_Version=GENCODE%20${GENCODE}'))
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL) - refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
......
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