diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index e66862ce5fe6bc9751597f9adf10747810161c04..c6178c4d58888c91e4fd086bf9e28a629133fb0d 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -240,8 +240,10 @@ humanDataHub: - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}) - curl --request GET ${query} > refQuery.json - refURL=$(python ./workflow/scripts/extractRefData.py) - ##- singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host ${referenceBase} get ${refURL} - - + - conda create --name deriva1.3 python=3.6 -y + - source activate deriva1.3 + - pip install deriva==1.3.0 --user + - deriva-hatrac-cli --host ${referenceBase} get ${refURL} mousenDataHub: stage: reference @@ -262,14 +264,12 @@ mousenDataHub: - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}) - curl --request GET ${query} > refQuery.json - refURL=$(python ./workflow/scripts/extractRefData.py) - ##- singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host ${referenceBase} get ${refURL} - conda create --name deriva1.3 python=3.6 -y - source activate deriva1.3 - pip install deriva==1.3.0 --user - deriva-hatrac-cli --host ${referenceBase} get ${refURL} - integration_se: stage: integration only: [merge_requests]