bamsurgeon.def

Bootstrap: docker
From: ubuntu:20.04

%labels
    AUTHOR_ORIGINAL_DOCKERFILE Adam Ewing <adam.ewing@gmail.com>
    AUTHOR_MODIFIED_SINGULARITY_DEF Julia Wiggeshoff <juliawiggeshoff@gmail.com>    

%environment
    export DEBIAN_FRONTEND=noninteractive
    export BAMSURGEON_PICARD_JAR=/usr/local/bin/picard.jar
    export PATH="/opt:/usr/local/bin:$PATH"
    LANG=C.UTF-8 LC_ALL=C.UTF-8

%post
    apt-get update && apt-get install -y --no-install-recommends tzdata 

    ln -fs /usr/share/zoneinfo/Europe/Berlin /etc/localtime 
    dpkg-reconfigure --frontend noninteractive tzdata

    apt-get update && apt-get upgrade -y && apt-get install -f -y \
        bzip2 \
        curl \
        python3 \
        python3-pip \
        git \
        wget \
        build-essential \
        libcurl4-openssl-dev \
        libncurses5-dev \
        libncursesw5-dev \
        libhts-dev \
        libz-dev \
        libglib2.0-dev \
        libbz2-dev \
        liblzma-dev \
        libjsoncpp-dev \
        libtabixpp-dev \
        libtabixpp0 \
        default-jre \
        autoconf \
        bwa \
        tabix \
        zlib1g
    
    cd /usr/local/src

    git clone --recurse-submodules --remote-submodules https://github.com/samtools/htslib.git
    git clone https://github.com/samtools/samtools.git
    git clone https://github.com/dzerbino/velvet.git
    git clone https://github.com/adamewing/exonerate.git
    
    wget https://github.com/broadinstitute/picard/releases/download/2.27.3/picard.jar
    chmod +x picard.jar && mv picard.jar /usr/local/bin

    cd htslib && autoreconf -i && ./configure --prefix=/usr/local && make && make install

    cd ../samtools && autoheader && autoconf -Wno-syntax && ./configure --prefix=/usr/local && make && make install && cp misc/wgsim /usr/local/bin    
    
    cd ../velvet && make && cp velvetg /usr/local/bin && cp velveth /usr/local/bin

    cd ../exonerate && git checkout v2.4.0 && autoreconf -i && ./configure --prefix=/usr/local && make && make check && make install

    cd / && mkdir -p /opt && cd /opt

    git clone https://github.com/adamewing/bamsurgeon.git
    sed -i 's#bam.header#bam.header.to_dict()#' bamsurgeon/scripts/postprocess.py
    
    cd / && pip install pysam

    apt-get clean

%runscript
    export PATH="/opt:/usr/local/bin:$PATH"