From a9d6c83a6ea8cd3de15a1fe3de06c3d4c30b53f2 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 17 Dec 2020 19:15:43 -0600
Subject: [PATCH] Try excaping sed characters
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 820b6d4..c50a61b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -331,9 +331,9 @@ uploadQC:
cookie=$(cat credential.json | grep -A 1 '"staging.gudmap.org\: {' | grep -o '"cookie": ".*"') &&
cookie=${cookie:11:-1} &&
if [ "${exist}" != "[]" ]; then
- rids=$(echo $exist | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//')
+ rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}\/\/')
for rid in ${rids}; do
- singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/deleteEntry.py -r ${rid} -t mRNA_QC -o $staging.gudmap.org -c ${cookie}
+ singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/deleteEntry.py -r ${rid} -t mRNA_QC -o $staging.gudmap.org -c ${cookie} &&
echo old mRNA QC RID deleted - ${rid}
done
echo all old mRNA QC RIDs deleted
--
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