From fcf86055fd8b832ac0f5a2a0a42f1b766670ddae Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 10 Sep 2020 19:57:37 -0500
Subject: [PATCH] Fix CI lint and replicate env in hu test
---
.gitlab-ci.yml | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e66862c..c6178c4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -240,8 +240,10 @@ humanDataHub:
- 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}
- -
+ - conda create --name deriva1.3 python=3.6 -y
+ - source activate deriva1.3
+ - pip install deriva==1.3.0 --user
+ - deriva-hatrac-cli --host ${referenceBase} get ${refURL}
mousenDataHub:
stage: reference
@@ -262,14 +264,12 @@ mousenDataHub:
- query=$(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}
- conda create --name deriva1.3 python=3.6 -y
- source activate deriva1.3
- pip install deriva==1.3.0 --user
- deriva-hatrac-cli --host ${referenceBase} get ${refURL}
-
integration_se:
stage: integration
only: [merge_requests]
--
GitLab