Dockerfile for hla-la version 1.0.3 built in alpine for fun. Inspired by https://github.com/zlskidmore/docker-hla-la

Dockerfile

FROM alpine
WORKDIR /usr/local/bin

# samtools
ENV samtools_version 1.16.1
RUN apk add g++ make ncurses-dev zlib-dev xz-dev bzip2-dev curl-dev
RUN wget https://github.com/samtools/samtools/releases/download/${samtools_version}/samtools-${samtools_version}.tar.bz2 && \
    tar -xjf samtools-${samtools_version}.tar.bz2 && \
    cd samtools-${samtools_version}/ && \
    ./configure && \
    make -j8 && \
    make install

# picard
ENV picard_version 1.123
RUN wget https://github.com/broadinstitute/picard/releases/download/${picard_version}/picard-tools-${picard_version}.zip && \
    unzip picard-tools-${picard_version}.zip && \
    mv picard-tools-${picard_version} picard/ && \
    chmod 0644 picard/SamToFastq.jar

# bwa
ENV bwa_version 0.7.17
RUN apk add g++ make zlib-dev
RUN wget https://github.com/lh3/bwa/archive/refs/heads/master.zip -O v${bwa_version}.zip && \
    unzip v${bwa_version}.zip && \
    rm -f v${bwa_version}.zip && \
    mv bwa-master bwa-${bwa_version} && \
    cd bwa-${bwa_version} && \
    make -j8 && \
    cd .. && \
    ln -s $PWD/bwa-${bwa_version}/bwa $PWD

# bamtools
ENV bamtools_version 2.5.1
RUN apk add g++ make cmake jsoncpp-dev zlib-dev
RUN wget https://github.com/pezmaster31/bamtools/archive/v${bamtools_version}.zip && \
    unzip v${bamtools_version}.zip && \
    rm    v${bamtools_version}.zip && \
    mkdir -p bamtools-${bamtools_version}/build && \
    cd bamtools-${bamtools_version}/build && \
    cmake -DCMAKE_INSTALL_PREFIX=$PWD/../../bamtools-${bamtools_version} .. && \
    make -j8 && \
    make install && \
    cd ../.. && \
    ln -s $PWD/bamtools-${bamtools_version}/lib $PWD/bamtools-${bamtools_version}/lib64
    
# HLA-LA
ENV hla_la_version 1.0.3
RUN apk add g++ make boost-dev
RUN mkdir -p HLA-LA/bin \
             HLA-LA/obj \
             HLA-LA/temp \
             HLA-LA/working \
             HLA-LA/graphs && \
    wget https://github.com/DiltheyLab/HLA-LA/archive/v${hla_la_version}.zip && \
    unzip v${hla_la_version}.zip && \
    mv HLA-LA-${hla_la_version} HLA-LA/src && \
    cd HLA-LA/src && \
    sed -i 's/u_int32_t/uint32_t/g' */*/*.cpp && \
    sed -i 's/u_int32_t/uint32_t/g' */*.cpp && \
    make all -j8 BOOST_PATH=/usr/include/boost BAMTOOLS_PATH=$PWD/../../bamtools-${bamtools_version}

RUN sed -i 's@samtools_bin=@samtools_bin=/usr/local/bin/samtools@' HLA-LA/src/paths.ini && \
    sed -i 's@bwa_bin=@bwa_bin=/usr/local/bin/bwa@' HLA-LA/src/paths.ini && \
    sed -i 's@picard_sam2fastq_bin=.*@picard_sam2fastq_bin=/usr/local/bin/picard/SamToFastq.jar@' HLA-LA/src/paths.ini

# runtime
RUN apk add perl openjdk11-jre
ENV PATH=/usr/local/bin/HLA-LA/src:/usr/local/bin/HLA-LA/bin:$PATH