nf-core_modules/modules/ensemblvep/Dockerfile

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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
# Setup default ARG variables
ARG GENOME=GRCh38
ARG SPECIES=homo_sapiens
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ARG VEP_VERSION=104
ARG VEP_TAG=104.3
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-vep-${VEP_TAG}/bin:$PATH
# Download Genome
RUN vep_install \
-a c \
-c .vep \
-s ${SPECIES} \
-y ${GENOME} \
--CACHE_VERSION ${VEP_VERSION} \
--CONVERT \
--NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE
# Dump the details of the installed packages to a file for posterity
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RUN conda env export --name nf-core-vep-${VEP_TAG} > nf-core-vep-${VEP_TAG}.yml