FROM ubuntu:18.04

MAINTAINER Ai Okada <aokada@ncc.go.jp>

RUN apt-get update && apt-get install -y \
    git \
    wget \
    bzip2 \
    make \
    gcc \
    zlib1g-dev \
    libbz2-dev \
    liblzma-dev \
    libcurl4-openssl-dev \
    libssl-dev \
    python \
    python3 \
    python3-pip

WORKDIR /tools

##########
# samtools etc

RUN wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 && \
    tar jxvf samtools-1.9.tar.bz2 && \
    cd samtools-1.9/htslib-1.9 && ./configure && make && make install && \
    cd ../ && ./configure --without-curses && make && make install

RUN wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 && \
    tar jxvf bcftools-1.9.tar.bz2 && \
    cd bcftools-1.9 && ./configure && make && make install

RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.27.0/bedtools-2.27.0.tar.gz && \
    tar -zxvf bedtools-2.27.0.tar.gz && \
    cd bedtools2 && make && make install

##########
# minimap

RUN wget https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17.tar.bz2 && \
    tar jxvf minimap2-2.17.tar.bz2 && \
    cd  minimap2-2.17 && make && mv minimap2 /usr/local/bin

ENV LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH

CMD ["/bin/bash"]