From eb32e8de56929d587d0cb936ea41b892c39de677 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 21 Jul 2021 20:28:23 -0500
Subject: [PATCH] Temporarily add -u to uploadOutputBag CI
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0a92cf9..7926735 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -548,7 +548,7 @@ uploadOutputBag:
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
loc=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt --parents) &&
- rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_output_bag.py -e ${ci_staging_rid_test_erun} -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) &&
+ rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_output_bag.py -e ${ci_staging_rid_test_erun} -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) -u "F" &&
echo ${rid} test output bag created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
--
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