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Dockerfile
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FROM jupyter/scipy-notebook:latest
# reset user to root for installing additional packages
USER root
COPY jupyter_notebook_config.json /opt/conda/etc/jupyter/jupyter_notebook_config.json
# Add project files
COPY environment.yml /home/jovyan/environment.yml
COPY Snakefile_mrsa /home/jovyan/Snakefile_mrsa
COPY config.yml /home/jovyan/config.yml
COPY code /home/jovyan/code
# Use bash as shell
SHELL ["/bin/bash", "-c"]
# Install a few dependencies for iCommands, text editing, and monitoring instances
RUN apt-get update && apt-get install -y \
apt-transport-https \
gcc \
gnupg \
htop \
less \
libfuse2 \
libpq-dev \
libssl1.0 \
lsb \
nano \
nodejs \
python-requests \
software-properties-common \
vim \
wget \
curl \
bzip2 \
ca-certificates \
fontconfig \
git \
language-pack-en \
tzdata \
unzip \
&& apt-get clean
# Install iCommands
RUN wget https://files.renci.org/pub/irods/releases/4.1.12/ubuntu14/irods-icommands-4.1.12-ubuntu14-x86_64.deb && \
dpkg -i irods-icommands-4.1.12-ubuntu14-x86_64.deb && \
rm irods-icommands-4.1.12-ubuntu14-x86_64.deb
# reset container user to jovyan
USER jovyan
# Install conda environment
RUN conda config --add channels bioconda && \
conda config --add channels conda-forge && \
conda env update -n base -f environment.yml && \
conda clean --all
# set the work directory
WORKDIR /home/jovyan/
# Open port for running Jupyter Notebook
# (Jupyter Notebook has to be separately installed in the container)
EXPOSE 8888
ENTRYPOINT ["jupyter"]
CMD snakemake -rp --configfile config.yml
CMD ["lab", "--no-browser"]