From df0f368bbe28b34de9ea367acc0a1204746e4696 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 13 Sep 2020 10:22:39 -0500
Subject: [PATCH] Split grep from pipe from python

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

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a8f136b..1e104e3 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -241,7 +241,8 @@ humanDataHub:
   - curl --request GET ${query} > refQuery.json
   - refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
   - refMD5=$(python ./workflow/scripts/extractRefData.py --returnParam MD5)
-  - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls /hatrac/resources/rnaseq/pipeline/reference_genome/ | grep -o ${refMD5})
+  - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls /hatrac/resources/rnaseq/pipeline/reference_genome/)
+  - test=$(echo ${test} | grep -o ${refMD5})
   - if [ "${test}" == "" ]; then exit 1; fi
 
 mousenDataHub:
@@ -264,7 +265,8 @@ mousenDataHub:
   - curl --request GET ${query} > refQuery.json
   - refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL)
   - refMD5=$(python ./workflow/scripts/extractRefData.py --returnParam MD5)
-  - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls /hatrac/resources/rnaseq/pipeline/reference_genome/ | grep -o ${refMD5})
+  - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls /hatrac/resources/rnaseq/pipeline/reference_genome/)
+  - test=$(echo ${test} | grep -o ${refMD5})
   - if [ "${test}" == "" ]; then exit 1; fi
 
 
-- 
GitLab