diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index ee12e643f6470a80c6f6f1f5b849eb943a3a1710..e66862ce5fe6bc9751597f9adf10747810161c04 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -240,7 +240,8 @@ 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} + ##- singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host ${referenceBase} get ${refURL} + - mousenDataHub: stage: reference @@ -261,7 +262,12 @@ mousenDataHub: - query=$(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} + ##- 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: