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Dockerfile
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FROM quay.io/wtsicgp/pcap-core:5.4.2 as builder
USER root
# ALL tool versions used by opt-build.sh
ENV VER_VCFTOOLS="0.1.16"
ENV VER_CGPVCF="v2.2.1"
ENV VER_CAVEMAN="1.15.5"
ENV VER_BEDTOOLS="2.27.1"
ENV VER_CGPCAVEPOSTPROC="1.12.0"
RUN apt-get -yq update
RUN apt-get install -yq --no-install-recommends locales
RUN apt-get install -yq --no-install-recommends g++
RUN apt-get install -yq --no-install-recommends make
RUN apt-get install -yq --no-install-recommends gcc
RUN apt-get install -yq --no-install-recommends pkg-config
RUN apt-get install -yq --no-install-recommends python
RUN apt-get install -yq --no-install-recommends zlib1g-dev
RUN apt-get install -yq --no-install-recommends libbz2-dev
RUN apt-get install -yq --no-install-recommends liblzma-dev
RUN apt-get install -yq --no-install-recommends libcurl4-openssl-dev
RUN apt-get install -yq --no-install-recommends wget
RUN apt-get install -yq --no-install-recommends unzip
RUN locale-gen en_US.UTF-8
RUN update-locale LANG=en_US.UTF-8
ENV OPT /opt/wtsi-cgp
ENV PATH $OPT/bin:$OPT/biobambam2/bin:$PATH
ENV PERL5LIB $OPT/lib/perl5
ENV LD_LIBRARY_PATH $OPT/lib
ENV C_INCLUDE_PATH $OPT/include/
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
# build tools from other repos
ADD build/opt-build.sh build/
RUN bash build/opt-build.sh $OPT
# build the tools in this repo, separate to reduce build time on errors
COPY . .
RUN bash build/opt-build-local.sh $OPT
FROM ubuntu:20.04
LABEL maintainer="[email protected]" \
uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
version="1.19.0" \
description="cgpCaVEManWrapper docker"
RUN apt-get -yq update
RUN apt-get install -yq --no-install-recommends \
locales \
curl \
ca-certificates \
libperlio-gzip-perl \
bzip2 \
psmisc \
time \
zlib1g \
liblzma5 \
libncurses5 \
p11-kit \
libcurl3-gnutls \
libcurl4 \
moreutils \
google-perftools \
unattended-upgrades && \
unattended-upgrade -d -v && \
apt-get remove -yq unattended-upgrades && \
apt-get autoremove -yq
RUN locale-gen en_US.UTF-8
RUN update-locale LANG=en_US.UTF-8
ENV OPT /opt/wtsi-cgp
ENV PATH $OPT/bin:$OPT/biobambam2/bin:$PATH
ENV PERL5LIB $OPT/lib/perl5
ENV LD_LIBRARY_PATH $OPT/lib
ENV C_INCLUDE_PATH $OPT/include/
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
RUN mkdir -p $OPT
COPY --from=builder $OPT $OPT
## USER CONFIGURATION
RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir -p /home/ubuntu
USER ubuntu
WORKDIR /home/ubuntu
CMD ["/bin/bash"]