diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index c6178c4d58888c91e4fd086bf9e28a629133fb0d..19337361bceb8415ad44c1b05258d41ae0ef1c9d 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,5 +1,5 @@ before_script: - - module add python/3.6.4-anaconda + - module load python/3.6.4-anaconda - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1 - module load singularity/3.5.3 - module load nextflow/20.01.0 @@ -240,7 +240,7 @@ 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) - - conda create --name deriva1.3 python=3.6 -y + - conda create --name deriva1.3 python=3.6 -y --no-deps - source activate deriva1.3 - pip install deriva==1.3.0 --user - deriva-hatrac-cli --host ${referenceBase} get ${refURL} @@ -264,7 +264,7 @@ mousenDataHub: - query=$(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) - - conda create --name deriva1.3 python=3.6 -y + - conda create --name deriva1.3 python=3.6 -y --no-deps - source activate deriva1.3 - pip install deriva==1.3.0 --user - deriva-hatrac-cli --host ${referenceBase} get ${refURL}