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Dockerfile
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FROM nfcore/base:1.9
LABEL authors="Sarai Varona and Sara Monzon" \
description="Docker image containing all software requirements for the nf-core/viralrecon pipeline"
# Install the conda environment
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
#RUN conda install -c conda-forge r-aws.s3 r-tidyr r-tidyverse r-optparse r-stringr r-dplyr r-stringi r-dbplyr r-dbi r-rmysql
# For Bandage: otherwise it complains about missing libGL.so.1
RUN apt-get update -y
RUN apt-get install -y sendmail libtbb-dev
RUN apt-get install -y libgl1-mesa-glx && apt-get clean -y
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-viralrecon-1.1.0/bin:$PATH
# Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-viralrecon-1.1.0 > nf-core-viralrecon-1.1.0.yml
# Instruct R processes to use these empty files instead of clashing with a local version
RUN touch .Rprofile
RUN touch .Renviron