FROM nfcore/base:1.14 LABEL \ author="Maxime Garcia" \ description="VEP image for nf-core pipelines" \ maintainer="maxime.garcia@scilifelab.se" # Install the conda environment COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') ENV PATH /opt/conda/envs/nf-core-vep-104.3/bin:$PATH # Setup default ARG variables ARG GENOME=GRCh38 ARG SPECIES=homo_sapiens ARG VEP_VERSION=99 # Download Genome RUN vep_install \ -a c \ -c .vep \ -s ${SPECIES} \ -y ${GENOME} \ --CACHE_VERSION ${VEP_VERSION} \ --CONVERT \ --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE # Dump the details of the installed packages to a file for posterity RUN conda env export --name nf-core-vep-104.3 > nf-core-vep-104.3.yml