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FROM ubuntu:24.04 as builder
USER root
ARG VER_BIODBHTS="3.01"
ARG VER_HTSLIB="1.9"
ARG VER_SAMTOOLS="1.9"
ENV VER_VCFTOOLS="0.1.16"
RUN apt-get -yq update
RUN apt-get install -yq --no-install-recommends
RUN apt-get install -yq --no-install-recommends apt-transport-https
RUN apt-get install -yq --no-install-recommends locales
RUN apt-get install -yq --no-install-recommends curl
RUN apt-get install -yq --no-install-recommends ca-certificates
RUN apt-get install -yq --no-install-recommends libperlio-gzip-perl
RUN apt-get install -yq --no-install-recommends make
RUN apt-get install -yq --no-install-recommends bzip2
RUN apt-get install -yq --no-install-recommends gcc
RUN apt-get install -yq --no-install-recommends psmisc
RUN apt-get install -yq --no-install-recommends time
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-gnutls-dev
RUN apt-get install -yq --no-install-recommends libncurses5-dev
RUN apt-get install -yq --no-install-recommends libgnutls28-dev
RUN apt-get install -yq --no-install-recommends libgd-dev
RUN apt-get install -yq --no-install-recommends libdb-dev
RUN apt-get install -yq --no-install-recommends g++
RUN apt-get install -yq --no-install-recommends libssl-dev
RUN apt-get install -yq --no-install-recommends xz-utils
RUN apt-get install -yq --no-install-recommends libxml2
RUN locale-gen en_US.UTF-8
RUN update-locale LANG=en_US.UTF-8
ENV OPT /opt/wtsi-cgp
ENV PERL5LIB $OPT/lib/perl5
ENV LD_LIBRARY_PATH $OPT/lib
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
RUN mkdir -p $OPT/bin
WORKDIR /install_tmp
ADD build/opt-build.sh build/
RUN bash build/opt-build.sh $OPT
COPY . .
RUN bash build/opt-build-local.sh $OPT
FROM ubuntu:24.04
LABEL maintainer="[email protected]"\
uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute" \
description="vafCorrect"
ENV OPT /opt/wtsi-cgp
ENV PATH $OPT/bin:$PATH
ENV PERL5LIB $OPT/lib/perl5
ENV LD_LIBRARY_PATH $OPT/lib
ENV LC_ALL C
RUN apt-get -yq update
RUN apt-get install -yq --no-install-recommends \
apt-transport-https \
locales \
curl \
ca-certificates \
libperlio-gzip-perl \
bzip2 \
psmisc \
time \
zlib1g \
liblzma5 \
libncurses6 \
exonerate \
openssl \
adduser \
libdeflate0 \
unattended-upgrades && \
unattended-upgrade -d -v && \
apt-get remove -yq unattended-upgrades && \
apt-get autoremove -yq
#RUN apt-get install -yq libdevel-nytprof-perl
RUN mkdir -p $OPT
COPY --from=builder $OPT $OPT
## USER CONFIGURATION
RUN chsh -s /bin/bash && mkdir -p /home/ubuntu
USER ubuntu
WORKDIR /home/ubuntu
CMD ["/bin/bash"]