diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index fe996a1cf043771492b287a462aa1a19b04edf08..19eea9323f881196b3dc7f4f5b91feea88e2072f 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,6 +1,6 @@ before_script: - module load python/3.6.4-anaconda - - pip install --user attrs==19.1.0 pytest-pythonpath==0.7.1 pytest-cov==2.5.1 + - pip install --user attrs==19.1.0 pytest-pythonpath==0.7.1 pytest-cov==2.5.1 deriva==1.3.0 - module load singularity/3.5.3 - module load nextflow/20.01.0 - ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/ @@ -240,7 +240,6 @@ 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) - - pip install --user deriva==1.3.0 - deriva-hatrac-cli --host ${referenceBase} get ${refURL} mousenDataHub: