analyzebam_cpp_dockerfile

FROM ubuntu:latest

ENV LD_LIBRARY_PATH="/r1/people/bioinf/src/htslib-1.4"
ENV CPLUS_INCLUDE_PATH="/r1/people/bioinf/src/htslib-1.4"

RUN apt-get update && \
    apt-get install -y software-properties-common && \
    apt-add-repository ppa:git-core/ppa && \
    apt-get update
 
RUN apt-get install -y gcc g++ git make wget bzip2 libbz2-dev \
    zlib1g-dev libncurses5-dev libncursesw5-dev liblzma-dev \
    libcurl4-gnutls-dev autoconf

RUN mkdir -p /r1/people/bioinf/src/ &&\
    cd /r1/people/bioinf/src/ &&\
    wget https://github.com/samtools/htslib/releases/download/1.4/htslib-1.4.tar.bz2 && \
    tar -xvjf htslib-1.4.tar.bz2 && \
    cd htslib-1.4 && \
    autoreconf -i && \
    make && \
    make install
    
RUN cd &&\
    git clone --revision=97714ed00e354851c56e577e11c8b3f356ce1279 https://github.com/yanivsw/ancient_dna_cpp_tools && \
    cd ancient_dna_cpp_tools && \
    make && \
    cp *BAM /usr/local/bin/

CMD ["analyzeBAM"]