Dockerfile

FROM ubuntu:22.04
WORKDIR /opt

ARG DEBIAN_FRONTEND=noninteractive
ARG MULTIMAPPER_BUILD_DIR=multimapper
LABEL maintainer=path-help@sanger.ac.uk

RUN apt update -qq -y && \
    apt install -y \
    locales \
    python3 \
    python3-setuptools \
    python3-pip \
    wget \
    make \
    git \
    g++ \
    meson \
    samtools \
    bcftools \
    freebayes \
    unzip \
    && apt clean -y

#Install smalt
RUN wget http://sourceforge.net/projects/smalt/files/smalt-0.7.6-static.tar.gz/download \
        && tar -zxvf download \
        && cd smalt-0.7.6 \
        && ./configure \
        && make \
        && make install \
        && cd ~
ENV PATH="/opt/smalt-0.7.6:$PATH"

#Install BWA-mem2
RUN git clone https://github.com/bwa-mem2/bwa-mem2 \
        && cd bwa-mem2 \
        && git submodule init \
        && git submodule update \
        && make \
        && cd ~
ENV PATH="$PATH:/opt/bwa-mem2/"

#Install RAxML-NG
RUN wget https://github.com/amkozlov/raxml-ng/releases/download/1.1.0/raxml-ng_v1.1.0_linux_x86_64.zip \
        && unzip raxml-ng_v1.1.0_linux_x86_64.zip
# Put binary on PATH
ENV PATH=/opt/raxml-ng:${PATH}

#Install java-19
RUN wget https://download.oracle.com/java/19/latest/jdk-19_macos-x64_bin.tar.gz \
        && tar -xvf jdk-19_macos-x64_bin.tar.gz -C /opt \
        && update-alternatives --install /usr/bin/java java /opt/jdk-19.0.2.jdk/Contents/Home/bin/java 1000 \
        && update-alternatives --install /usr/bin/javac javac /opt/jdk-19.0.2.jdk/Contents/Home/bin/javac 1000 \
        && update-alternatives --config java \
        && update-alternatives --config javac

#Install Sambamba
#ARG LDC=1.30.0
#RUN wget https://github.com/ldc-developers/ldc/releases/download/v$LDC/ldc2-1.7.0-linux-x86_64.tar.xz \
#        && tar xvJf ldc2-1.7.0-linux-x86_64.tar.xz \
#        && export PATH=$HOME/ldc2-1.7.0-linux-x86_64/bin:$PATH \
#        && export LIBRARY_PATH=$HOME/ldc2-1.7.0-linux-x86_64/lib \
#        && git clone --recursive https://github.com/biod/sambamba.git \
#        && cd sambamba \
#        && make

#Install Bowtie2
RUN wget https://github.com/BenLangmead/bowtie2/archive/refs/tags/v2.5.1.tar.gz \
    && tar -xvf v2.5.1.tar.gz \
    && cd bowtie2-2.5.1 \
    && make \
    && make static-libs \
    && make STATIC_BUILD=1
ENV PATH=/opt/bowtie2-v2.5.1:${PATH}

# Install multimapper
RUN mkdir -p $MULTIMAPPER_BUILD_DIR
COPY . $MULTIMAPPER_BUILD_DIR
RUN cd $MULTIMAPPER_BUILD_DIR \
    && apt install -y libbz2-dev liblzma-dev \
    && pip3 install biopython \
    matplotlib \
    numpy \
    pysam \