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Add iRODS 4.3-nightly client development image
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| # syntax=docker/dockerfile:1 | ||
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| ARG BASE_IMAGE=ubuntu:16.04 | ||
| FROM $BASE_IMAGE as installer | ||
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| ARG IRODS_VERSION="4.2.7" | ||
| ARG BATON_VERSION="4.1.0" | ||
| ARG HTSLIB_VERSION="1.18" | ||
| ARG SAMTOOLS_VERSION="1.18" | ||
| ARG BCFTOOLS_VERSION="1.18" | ||
| ARG HTSLIB_PLUGINS_VERSION="201712" | ||
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| COPY . /opt/docker/irods_clients | ||
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| RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections && \ | ||
| apt-get update && \ | ||
| apt-get install -q -y --no-install-recommends \ | ||
| apt-transport-https \ | ||
| apt-utils \ | ||
| ca-certificates \ | ||
| curl \ | ||
| dirmngr \ | ||
| gnupg \ | ||
| gnupg-agent \ | ||
| lsb-release \ | ||
| locales && \ | ||
| locale-gen en_GB en_GB.UTF-8 && \ | ||
| localedef -i en_GB -c -f UTF-8 -A /usr/share/locale/locale.alias en_GB.UTF-8 | ||
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| ENV LANG=en_GB.UTF-8 \ | ||
| LANGUAGE=en_GB \ | ||
| LC_ALL=en_GB.UTF-8 | ||
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| RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - && \ | ||
| echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" |\ | ||
| tee /etc/apt/sources.list.d/renci-irods.list && \ | ||
| apt-get update && \ | ||
| apt-get install -q -y --no-install-recommends \ | ||
| irods-dev="${IRODS_VERSION}" \ | ||
| irods-runtime="${IRODS_VERSION}" \ | ||
| irods-icommands="${IRODS_VERSION}" | ||
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| RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys "E1DD270288B4E6030699E45FA1715D88E1DF1F24" && \ | ||
| echo "deb https://ppa.launchpadcontent.net/git-core/ppa/ubuntu $(lsb_release -sc) main" |\ | ||
| tee /etc/apt/sources.list.d/git-core.list && \ | ||
| apt-get update && \ | ||
| apt-get install -q -y --no-install-recommends \ | ||
| git | ||
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| # libdeflate-dev is not available on Ubuntu 16.04 | ||
| RUN apt-get update && \ | ||
| apt-get install -q -y --no-install-recommends \ | ||
| autoconf \ | ||
| automake \ | ||
| build-essential \ | ||
| less \ | ||
| libtool \ | ||
| pkg-config \ | ||
| python3-sphinx \ | ||
| ssh \ | ||
| libjansson-dev \ | ||
| libbz2-dev \ | ||
| libcurl3-dev \ | ||
| liblzma-dev \ | ||
| zlib1g-dev | ||
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| ENV CPPFLAGS="-I/usr/include/irods" | ||
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| RUN cd /tmp && \ | ||
| curl -sSL -O "https://github.com/wtsi-npg/baton/releases/download/${BATON_VERSION}/baton-${BATON_VERSION}.tar.gz" && \ | ||
| tar xfz baton-${BATON_VERSION}.tar.gz && \ | ||
| cd baton-${BATON_VERSION} && \ | ||
| ./configure && \ | ||
| make install | ||
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| RUN cd /tmp && \ | ||
| curl -sSL -O "https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2" && \ | ||
| tar xfj htslib-${HTSLIB_VERSION}.tar.bz2 && \ | ||
| cd htslib-${HTSLIB_VERSION} && \ | ||
| ./configure --enable-plugins --without-curses && \ | ||
| make install && \ | ||
| ldconfig | ||
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| RUN cd /tmp && \ | ||
| curl -sSL -O "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" && \ | ||
| tar xfj samtools-${SAMTOOLS_VERSION}.tar.bz2 && \ | ||
| cd samtools-${SAMTOOLS_VERSION} && \ | ||
| ./configure --with-htslib=system --without-curses && \ | ||
| make install | ||
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| RUN cd /tmp && \ | ||
| curl -sSL -O "https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2" && \ | ||
| tar xfj bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \ | ||
| cd bcftools-${BCFTOOLS_VERSION} && \ | ||
| ./configure --with-htslib=system --without-curses && \ | ||
| make install | ||
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| RUN cd /tmp && \ | ||
| git clone --depth 1 --branch ${HTSLIB_PLUGINS_VERSION} "https://github.com/samtools/htslib-plugins.git" && \ | ||
| cd htslib-plugins && \ | ||
| make install | ||
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| FROM $BASE_IMAGE | ||
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| ARG DOCKER_IMAGE | ||
| ARG DOCKER_TAG | ||
| ARG IRODS_VERSION="4.2.7" | ||
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| RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections && \ | ||
| apt-get update && \ | ||
| apt-get install -q -y --no-install-recommends \ | ||
| apt-transport-https \ | ||
| apt-utils \ | ||
| ca-certificates \ | ||
| curl \ | ||
| dirmngr \ | ||
| gnupg \ | ||
| gnupg-agent \ | ||
| lsb-release \ | ||
| locales && \ | ||
| locale-gen en_GB en_GB.UTF-8 && \ | ||
| localedef -i en_GB -c -f UTF-8 -A /usr/share/locale/locale.alias en_GB.UTF-8 | ||
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| ENV LANG=en_GB.UTF-8 \ | ||
| LANGUAGE=en_GB \ | ||
| LC_ALL=en_GB.UTF-8 | ||
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| RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - && \ | ||
| echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" |\ | ||
| tee /etc/apt/sources.list.d/renci-irods.list && \ | ||
| apt-get update && \ | ||
| apt-get install -q -y --no-install-recommends \ | ||
| irods-runtime="${IRODS_VERSION}" \ | ||
| irods-icommands="${IRODS_VERSION}" | ||
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| RUN apt-get install -q -y --no-install-recommends \ | ||
| gnuplot \ | ||
| jq \ | ||
| libjansson4 \ | ||
| libbz2-1.0 \ | ||
| libcurl3 \ | ||
| liblzma5 \ | ||
| perl \ | ||
| zlib1g \ | ||
| unattended-upgrades && \ | ||
| unattended-upgrade -v && \ | ||
| apt-get remove -q -y unattended-upgrades && \ | ||
| apt-get autoremove -q -y && \ | ||
| apt-get clean -q -y && \ | ||
| rm -rf /var/lib/apt/lists/* | ||
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| # Copy the installed baton and samtools applications | ||
| COPY --from=installer /usr/local /usr/local | ||
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| # Copy the singularity-wrapper scripts | ||
| COPY --from=singularity ./scripts/* /usr/local/bin/ | ||
| COPY --from=installer /opt/docker/irods_clients/manifest.json /usr/local/irods_clients/etc/manifest.json | ||
| COPY --from=installer /opt/docker/irods_clients/scripts/docker-entrypoint.sh /usr/local/irods_clients/bin/docker-entrypoint.sh | ||
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| # Configure the singularity-wrapper script | ||
| ENV MANIFEST_PATH="/usr/local/irods_clients/etc/manifest.json" | ||
| ENV DOCKER_IMAGE="$DOCKER_IMAGE" | ||
| ENV DOCKER_TAG="$DOCKER_TAG" | ||
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| RUN ldconfig | ||
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| ENTRYPOINT ["/usr/local/irods_clients/bin/docker-entrypoint.sh"] | ||
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| CMD ["/bin/bash"] |
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