From e84a5f047dfe83e84ee3fe5629fdc2f09cf50907 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 10 Sep 2020 19:53:36 -0500
Subject: [PATCH] Create deriva python env in ci until deriva1.3 docker image
available
---
.gitlab-ci.yml | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ee12e64..e66862c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -240,7 +240,8 @@ 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}
+ ##- singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host ${referenceBase} get ${refURL}
+ -
mousenDataHub:
stage: reference
@@ -261,7 +262,12 @@ mousenDataHub:
- query=$(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}
+ ##- 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:
--
GitLab