diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 990d92e7751a80042d967b5c8b6a2b34e0afc1c2..33d08440694670db5306e8a0980d38a67198701a 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -291,7 +291,7 @@ uploadInputBag: hatrac=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o /TESTX$) && echo ${hatrac} && if [ -z "${hatrac}" ]; then - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TESTX && + singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TESTX fi - echo THIS IS A TEST FILE > test.txt - > @@ -303,7 +303,7 @@ uploadInputBag: cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && cookie=${cookie:11:-1} && loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt) && - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie} && + singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie} fi