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Dockerfile
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Dockerfile
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# Make sure to start with a .dockerignore file that contains at least .git (see file in this repo)
# To build the docker container, run
#
# docker build . -t <username>/<repo_name>:<version>
#
# Once you've tested the container and are ready to publish, run
#
# docker push <username>/<repo_name>:<version>
#
# Start with PyModulon base container
FROM sbrg/pymodulon:v0.2.1
# Add your contact information
LABEL maintainer="Anand Sastry <[email protected]>"
# Change to root user for installation
USER root
# Install R
RUN apt-get update --yes && \
# Install R dependencies
apt-get install --yes --no-install-recommends \
gfortran \
liblapack-dev \
libopenblas-dev && \
# Clean up
apt-get clean && rm -rf /var/lib/apt/lists/*
# Install R libraries
RUN conda install --quiet --yes -c conda-forge -c bioconda \
'r-base=4.1.0' \
'r-irkernel=1.2*' \
'r-treemap=2.4*' \
'r-venndiagram=1.6*' && \
conda clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
# Change user back to NB_USER
USER $NB_USER
# Copy the repository to the container. Make sure your .dockerignore file skips any unnecessarily large files
COPY --chown=$NB_USER:$NB_GID . /home/${NB_USER}/modulome-nextflow
# Make sure to test your container and ensure that everything runs!