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