Singularity.snapperdb_v3

Bootstrap: docker
From: postgres:11

%post
    apt-get -y update && apt-get -y upgrade
    apt-get -y install curl git make procps
    apt-get -y install bzip2 libbz2-dev g++ libncurses5-dev openjdk-8-jdk-headless unzip liblzma-dev zlib1g-dev
    apt-get -y install python-dev python-pip

    pip install cython
    pip install argparse bintrees biopython psycopg2-binary paramiko PyVCF PyYAML hashids joblib

    pip install git+https://github.com/m-bull/PHEnix.git
    
    cd /opt
    git clone https://github.com/connor-lab/snapper3.git
   
    # SAMtools
    curl -fsSL 'https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2' | tar -xj -C /tmp/
    cd /tmp/samtools-1.9 && ./configure && make && make install
    rm -rf /tmp/samtools-1.9

    # BCFtools
    curl -fsSL 'https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2' | tar -xj -C /tmp/
    cd /tmp/bcftools-1.9 && ./configure && make && make install
    rm -rf /tmp/bcftools-1.9

    # HTSLib
    curl -fsSL 'https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2' | tar -xj -C /tmp/
    cd /tmp/htslib-1.9 && ./configure && make && make install
    rm -rf /tmp/htslib-1.9

    # Minimap2
    cd /tmp
    git clone https://github.com/lh3/minimap2 /tmp/minimap2
    cd /tmp/minimap2
    make
    mv /tmp/minimap2/minimap2 /usr/local/bin/
    rm -rf /tmp/minimap2

    # BWA
    cd /tmp
    git clone https://github.com/lh3/bwa /tmp/bwa
    cd /tmp/bwa
    make
    mv /tmp/bwa/bwa /usr/local/bin/
    rm -rf /tmp/bwa

    # Picard
    curl -fsSL 'https://github.com/broadinstitute/picard/releases/download/2.18.16/picard.jar' --output /usr/local/bin/picard.jar

    # GATK
    curl -fsSL 'https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef' | tar -xj -C /usr/local/bin
    find /usr/local/bin/GenomeAnalysisTK* -name "GenomeAnalysisTK.jar" -exec ln -s {} /usr/local/bin \;

%environment
    export PICARD_JAR=/usr/local/bin/picard.jar
    export GATK_JAR=/usr/local/bin/GenomeAnalysisTK.jar
    export PATH=/opt/snapper3/scripts:$PATH
    export PYTHONPATH=/opt/snapper3:/opt/snapper3/scripts:$PYTHONPATH

%labels
    Maintainer m-bull
    Version snapperdb-m-bull-git-latest