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Dockerfile
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FROM ubuntu:focal-20220113
ENV DEBIAN_FRONTEND=noninteractive
# Must install this because gpg not installed
RUN apt-get update && \
apt-get install -y --no-install-recommends \
software-properties-common \
dirmngr \
wget && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
#RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
# General sys dependencies
RUN apt-get update && apt-get install -y --allow-unauthenticated --no-install-recommends \
bedtools \
dos2unix \
python3 \
python3-pip \
python3-dev \
git \
r-base-core=4.3.3-1.2004.0 \
r-base-dev=4.3.3-1.2004.0 \
cmake \
curl \
# synapser client dependencies
dpkg-dev \
zlib1g-dev \
libssl-dev \
libffi-dev \
libcurl4-openssl-dev \
# VariantAnnotation dependency
libxml2-dev \
# Supports data guide creation
texlive \
texinfo \
# texlive-generic-recommended \
texlive-latex-extra \
# genome nexus
openjdk-11-jre \
# This is for reticulate
python3.8-venv && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
#install pandoc 1.19.2.1 (dashboard use)
# RUN wget https://github.com/jgm/pandoc/releases/download/1.19.2.1/pandoc-1.19.2.1-1-amd64.deb
# RUN dpkg -i pandoc-1.19.2.1-1-amd64.deb
RUN wget https://github.com/jgm/pandoc/releases/download/3.0.1/pandoc-3.0.1-1-amd64.deb
RUN dpkg -i pandoc-3.0.1-1-amd64.deb
# Only copy most recent changes in code are always installed
# Do not build from local computer
WORKDIR /root/Genie
# Copy install packages first, because R installation takes
# a long time and unless there are changes to the actual
# R packages used. So the only files copied over are
# renv/ renv.lock and the installation R script
COPY R/install_packages.R R/install_packages.R
COPY renv/ renv/
COPY renv.lock renv.lock
RUN Rscript R/install_packages.R
ENV CRYPTOGRAPHY_DONT_BUILD_RUST=true
COPY . .
RUN echo "source('renv/activate.R')" >> .Rprofile
# TODO Must include R/ and templates/ within the
# genie/ directory to use MANIFEST.in
# For now, install using develop parameter so that
# the package is called from the directory
RUN pip3 install --no-cache-dir -r requirements.txt
RUN python3 setup.py develop
# RUN pip3 install --no-cache-dir .
WORKDIR /root/
# Must move this git clone to after the install of Genie,
# because must update cbioportal
RUN git clone https://github.com/cBioPortal/cbioportal.git -b v5.3.19
RUN git clone https://github.com/Sage-Bionetworks/annotation-tools.git -b 0.0.5
WORKDIR /root/Genie