From 629f5f3eb544e124e199d97f871f31e022718e09 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 29 Dec 2020 15:31:33 -0600
Subject: [PATCH] Add back necessary ' in ref ci
---
.gitlab-ci.yml | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 88ec74e..783b0ca 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -458,8 +458,7 @@ human_dev:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(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}')
- - 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})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL})
@@ -484,7 +483,7 @@ mouse_dev:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(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})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL})
@@ -509,7 +508,7 @@ human_staging:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(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})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL})
@@ -535,7 +534,7 @@ mouse_staging:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(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})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL})
@@ -560,7 +559,7 @@ human_prod:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(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})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL})
@@ -586,7 +585,7 @@ mouse_prod:
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(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})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
- loc=$(dirname ${refURL})
--
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