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Dockerfile
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FROM quay.io/jupyter/r-notebook
USER root
RUN apt-get update
RUN apt-get install -y --fix-missing \
libssl-dev \
libcurl4-openssl-dev \
libxml2-dev \
glpk-utils \
libfontconfig1-dev \
libharfbuzz-dev \
libfribidi-dev \
libproj-dev \
libfreetype6-dev \
libpng-dev \
libtiff5-dev \
libjpeg-dev \
mono-mcs \
mono-xbuild \
mono-runtime \
libmono-system-data4.0-cil && \
conda install -y -c conda-forge glpk gmp && \
ln -s /opt/conda/include/libxml2/libxml /opt/conda/include/
RUN echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' >>/opt/conda/lib/R/etc/Rprofile.site
RUN R -e 'install.packages(c("BiocManager", "igraph"))'
RUN R -e 'BiocManager::install(c("clusterProfiler", "AnnotationDbi", "org.Hs.eg.db"), ask=FALSE, update=TRUE)'
EXPOSE 8888
RUN mkdir -p /etc/jupyter
RUN echo "c.NotebookApp.notebook_dir = '/app/notebooks'" >> /etc/jupyter/jupyter_lab_config.py
RUN echo "c.MappingKernelManager.kernel_cmd_timeout = 3600" >> /home/jovyan/.jupyter/jupyter_notebook_config.py
CMD ["jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]