58 lines
1.7 KiB
Docker
58 lines
1.7 KiB
Docker
FROM ubuntu:bionic
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ENV R_VERSION=3.6.3
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ENV ROCKER_VERSION=4.1.1
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ENV R_HOME=/usr/local/lib/R
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ENV TZ=Etc/UTC
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ENV SAMTOOLS_VERSION=1.2
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# Install R basic dependencies
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RUN apt-get update && \
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apt-get install --no-install-recommends -y \
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sed \
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curl \
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ca-certificates
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RUN curl -L "https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${ROCKER_VERSION}.tar.gz" | tar xvz
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RUN ./rocker-versioned2-R${ROCKER_VERSION}/scripts/install_R.sh
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RUN rm -rf rocker-versioned2-R${ROCKER_VERSION}
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# Install BioPerl
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RUN apt-get update && \
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apt-get install --no-install-recommends -y \
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curl \
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perl \
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cpanminus \
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build-essential \
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make \
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libexpat1-dev \
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libssl-dev \
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zlib1g-dev
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RUN cpanm -n -v Bio::Seq Bio::SeqIO Perl4::CoreLibs
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# Install R packages
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RUN install2.r --error --skipinstalled BiocManager
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RUN R -e "BiocManager::install(c('Biostrings', 'seqinr'))"
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# Install samtools
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RUN apt-get update && \
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apt-get install --no-install-recommends -y libncurses5-dev
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RUN curl -L "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" | tar xvj
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RUN cd samtools-${SAMTOOLS_VERSION} && make && make install && cd ..
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RUN rm -rf samtools-${SAMTOOLS_VERSION}
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# Cleanup
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RUN apt-get remove -y \
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build-essential \
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make
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# Install Viquas
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RUN apt-get update && apt-get install --no-install-recommends -y curl
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RUN mkdir /viquas && curl -L "https://master.dl.sourceforge.net/project/viquas/ViQuaS1.3.tar.gz" | tar xvz -C /viquas --strip-components=1
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RUN apt-get remove -y curl
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# Add wrapper script
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COPY viquas /usr/bin/viquas
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RUN chmod +x /usr/bin/viquas
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RUN mkdir /work
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ENTRYPOINT [ "viquas" ]
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