From 00983e2b720421cf09c4262eba435be496cfc204 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 9 Sep 2020 22:07:31 -0500
Subject: [PATCH] Fix CI lint
---
.gitlab-ci.yml | 46 +++++++++++++++++++++++-----------------------
1 file changed, 23 insertions(+), 23 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9c19340..0b2eab1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -9,7 +9,7 @@ before_script:
stages:
- unit
- - references
+ - reference
- integration
- consistency
@@ -229,17 +229,17 @@ humanDataHub:
except:
- merge_requests
script:
- referenceBase=dev.gudmap.org
- refName=GRCh
- refHuVersion=38.p12.v31
- references=$(echo ${referenceBase}/${refName}${refHuVersion})
- GRCv=$(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})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py)
- deriva-hatrac-cli --host ${referenceBase} get ${refURL}
+ - referenceBase=dev.gudmap.org
+ - refName=GRCh
+ - refHuVersion=38.p12.v31
+ - references=$(echo ${referenceBase}/${refName}${refHuVersion})
+ - GRCv=$(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})
+ - curl --request GET ${query} > refQuery.json
+ - refURL=$(python ./workflow/scripts/extractRefData.py)
+ - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host ${referenceBase} get ${refURL}
mousenDataHub:
stage: reference
@@ -249,17 +249,17 @@ mousenDataHub:
except:
- merge_requests
script:
- referenceBase=dev.gudmap.org
- refName=GRCm
- refHuVersion=38.p6.vM22
- references=$(echo ${referenceBase}/${refName}${refHuVersion})
- GRCv=$(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})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extractRefData.py)
- deriva-hatrac-cli --host ${referenceBase} get ${refURL}
+ - referenceBase=dev.gudmap.org
+ - refName=GRCm
+ - refHuVersion=38.p6.vM22
+ - references=$(echo ${referenceBase}/${refName}${refHuVersion})
+ - GRCv=$(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})
+ - curl --request GET ${query} > refQuery.json
+ - refURL=$(python ./workflow/scripts/extractRefData.py)
+ - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host ${referenceBase} get ${refURL}
integration_se:
--
GitLab