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Dockerfile
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FROM nfcore/base:1.12.1
LABEL authors="Maxime Garcia, Szilveszter Juhos" \
description="Docker image containing all software requirements for the nf-core/sarek pipeline"
# Install the conda environment
COPY environment.yml /
RUN conda env create --quiet -f /environment.yml && conda clean -a
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-sarek-2.7/bin:$PATH
# Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-sarek-2.7 > nf-core-sarek-2.7.yml
# Instruct R processes to use these empty files instead of clashing with a local version
RUN touch .Rprofile
RUN touch .Renviron