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Commit 0e1ef7f7 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Use non spike for CI ref tests

parent 683332a9
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2 merge requests!58Develop,!56Resolve "Detect error in inferMetadata for tracking"
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.gitlab-ci.yml
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...@@ -511,7 +511,7 @@ human_dev: ...@@ -511,7 +511,7 @@ 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=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
...@@ -537,7 +537,7 @@ mouse_dev: ...@@ -537,7 +537,7 @@ mouse_dev:
- GRCv=$(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=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
...@@ -563,7 +563,7 @@ human_staging: ...@@ -563,7 +563,7 @@ human_staging:
- GRCv=$(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=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
...@@ -590,7 +590,7 @@ mouse_staging: ...@@ -590,7 +590,7 @@ mouse_staging:
- GRCv=$(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=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
...@@ -616,7 +616,7 @@ human_prod: ...@@ -616,7 +616,7 @@ human_prod:
- GRCv=$(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=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
...@@ -643,7 +643,7 @@ mouse_prod: ...@@ -643,7 +643,7 @@ mouse_prod:
- GRCv=$(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=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
- curl --request GET ${query} > refQuery.json - curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL}) - loc=$(dirname ${refURL})
......
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