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# List of dependencies installed
# bcftools v1.9-1-deb_cv1
# ensemblorg/ensembl-vep:release_104.3
# python 2.7
# python 3.8.13
# R 4.2.1
# dc7a542b7e1f
#FROM ubuntu:18.04
FROM ensemblorg/ensembl-vep:release_104.3
USER root
ENV DEBIAN_FRONTEND noninteractive
# Install dependencies
RUN apt-get update && apt-get install -y \
curl \
git \
build-essential \
libncurses-dev \
zlib1g-dev \
libz-dev \
libbz2-dev \
liblzma-dev \
tabix \
python2.7 \
python3.8 \
python3.8-dev \
python3.8-distutils \
python3-apt
RUN curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
RUN python3.8 get-pip.py
# Install python 3.8 dependencies
COPY requirements.txt /opt/requirements.txt
RUN pip3 install --upgrade pip
RUN pip3 install -r /opt/requirements.txt
RUN pip3 install bgzip
# Install R
RUN apt-get update
RUN apt install -y --no-install-recommends software-properties-common dirmngr
# Add the keys
RUN apt install wget
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
# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
#RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
# apt-key adv --keyserver ha.pool.sks-keyservers.net --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
# apt-key adv --keyserver pgp.mit.edu --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
# apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
# apt-key adv --keyserver keyserver.pgp.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
#RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
RUN add-apt-repository universe
RUN apt-get update
RUN apt install -y r-base r-base-core
# Install R libs
RUN R -e "install.packages('data.table',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('dplyr',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('ontologyIndex',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('ontologySimilarity',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('tidyverse',dependencies=TRUE, repos='http://cran.rstudio.com/')"
# Install bcftools
RUN wget https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2
RUN mv bcftools-1.20.tar.bz2 /opt/bcftools-1.20.tar.bz2
RUN tar -xf /opt/bcftools-1.20.tar.bz2 -C /opt/ && \
rm /opt/bcftools-1.20.tar.bz2 && \
cd /opt/bcftools-1.20 && \
./configure && \
make && \
make install && \
rm -rf /opt/bcftools-1.20
# Install bedtools
RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary
RUN mv bedtools.static.binary /run/bedtools
RUN chmod a+x /run/bedtools