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