From 7548648304027b489ea0913fbd044dd3f9039496 Mon Sep 17 00:00:00 2001
From: Gervaise Henry <GHENRY@swmed.org>
Date: Tue, 18 Feb 2020 12:24:36 -0600
Subject: [PATCH] Update unit for getRef to use local refs

---
 .gitlab-ci.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2cc3b0c..0ae31f4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -38,8 +38,10 @@ parseMetadata:
 getRef:
   stage: unit
   script:
-  - singularity run 'docker://bicf/awscli:1.1' aws s3 ls s3://bicf-references/mouse/0.0.1/GRCm38.P6
-  - singularity run 'docker://bicf/awscli:1.1' aws s3 ls s3://bicf-references/human/0.0.1/GRCh38.p12
+  - 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
-- 
GitLab