From 97cd5936e76801fa4bc25b7897fb012250ac33e0 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 9 Sep 2020 22:04:16 -0500
Subject: [PATCH] Put getRef in CI stage and add get from datahub
---
.gitlab-ci.yml | 77 +++++++++++++++++++++++++++++++++++++++++---------
1 file changed, 64 insertions(+), 13 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1cf1103..9c19340 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -9,6 +9,7 @@ before_script:
stages:
- unit
+ - references
- integration
- consistency
@@ -74,19 +75,6 @@ inferMetadata:
if [[ ${ended} == "" ]]; then exit 1; fi
- pytest -m inferMetadata
-getRef:
- stage: unit
- only:
- - push
- - tags
- except:
- - merge_requests
- script:
- - mkdir -p hu
- - mkdir -p mo
- - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./hu/
- - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./mo/
-
trimData:
stage: unit
only:
@@ -211,6 +199,69 @@ outputBag:
- pytest -m outputBag
+humanBioHPC:
+ stage: reference
+ only:
+ - push
+ - tags
+ except:
+ - merge_requests
+ script:
+ - mkdir -p hu
+ - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./hu/
+
+mouseBioHPC:
+ stage: reference
+ only:
+ - push
+ - tags
+ except:
+ - merge_requests
+ script:
+ - mkdir -p mo
+ - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./mo/
+
+humanDataHub:
+ stage: reference
+ only:
+ - push
+ - tags
+ except:
+ - merge_requests
+ script:
+ referenceBase=dev.gudmap.org
+ refName=GRCh
+ refHuVersion=38.p12.v31
+ references=$(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 ${refURL}
+
+mousenDataHub:
+ stage: reference
+ only:
+ - push
+ - tags
+ except:
+ - merge_requests
+ script:
+ referenceBase=dev.gudmap.org
+ refName=GRCm
+ refHuVersion=38.p6.vM22
+ references=$(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}
+
+
integration_se:
stage: integration
only: [merge_requests]
--
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