Dockerfile.aarch64.base

FROM ubuntu:20.04

USER root

ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update -y && apt-get install cmake curl wget git gcc g++ make bzip2 -y
RUN apt install parallel libbz2-dev liblzma-dev zlib1g-dev libcurl4-openssl-dev -yy
RUN apt install python3 python3-pip rsync -yy

RUN mkdir /monorail_bin
ENV PATH="/monorail_bin:$PATH"
RUN mkdir /temp
WORKDIR /temp

RUN wget https://downloads.python.org/pypy/pypy2.7-v7.3.11-aarch64.tar.bz2
RUN bunzip2 pypy2.7-v7.3.11-aarch64.tar.bz2
RUN tar -xvf pypy2.7-v7.3.11-aarch64.tar
RUN rsync -av pypy2.7-v7.3.11-aarch64/* /monorail_bin/

RUN wget https://github.com/madler/pigz/archive/refs/tags/v2.4.tar.gz -O pigz-v2.4.tar.gz
RUN tar -zxvf pigz-v2.4.tar.gz
WORKDIR /temp/pigz-2.4 
RUN make
RUN rsync -av pigz unpigz /monorail_bin/
WORKDIR /temp

RUN apt install -yy snakemake=5.10.0-2

# install samtools
RUN apt-get install -y autoconf gcc make
ENV SM_VER=1.11
RUN curl -OL https://github.com/samtools/samtools/releases/download/${SM_VER}/samtools-${SM_VER}.tar.bz2 && \
    bzip2 -dc samtools-${SM_VER}.tar.bz2 | tar xvf - && \
    rm -f samtools-${SM_VER}.tar.bz2 && \
    cd samtools-${SM_VER} && \
    autoheader && \
    autoconf && \
    ./configure --disable-bz2 --disable-lzma --disable-libcurl --without-libdeflate --without-curses && \
    make && \
    make install

WORKDIR /temp/samtools-${SM_VER}/htslib-${SM_VER}
RUN make
RUN rsync -av tabix bgzip /monorail_bin/
WORKDIR /temp

RUN wget https://github.com/samtools/bcftools/archive/refs/tags/1.11.tar.gz -O bcftools-1.11.tar.gz
RUN tar -zxvf bcftools-1.11.tar.gz && \
    rm -f bcftools-1.11.tar.gz && \
    cd bcftools-${SM_VER} && \
    autoheader && \
    autoconf && \
    ./configure --with-htslib=/temp/samtools-${SM_VER}/htslib-${SM_VER} --disable-bz2 --disable-lzma --disable-libcurl --without-libdeflate --without-curses && \
    make && \
    make install

#zstd
#ZVER=1.4.2 
#faster than 1.3.3
ENV ZVER=1.3.3
RUN wget https://github.com/facebook/zstd/archive/refs/tags/v${ZVER}.tar.gz
RUN tar -zxvf v${ZVER}.tar.gz
RUN cd zstd-${ZVER} && make && rsync -av zstd /monorail_bin/

WORKDIR /

RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN apt-get clean
RUN apt-get autoremove -y
RUN rm -rf /var/lib/{apt,dpkg,cache,log}/ /temp