Singularity.ariba

Bootstrap: docker
From: centos:latest


%post
    yum -y update
    yum -y install epel-release
    yum install -y bzip2 bzip2-devel gcc gcc-c++ git ncurses-devel make unzip xz-devel zlib-devel
    yum install -y python36 python36-devel python36-setuptools

    easy_install-3.6 pip
  
    ## MUMmer 4 
    curl -fsSL 'https://github.com/mummer4/mummer/releases/download/v4.0.0beta2/mummer-4.0.0beta2.tar.gz' | tar -xz -C /usr/local/bin
    cd /usr/local/bin/mummer-4.0.0beta2 && ./configure && make install
 
    ## Bowtie2
    curl -fsSL 'https://github.com/BenLangmead/bowtie2/releases/download/v2.3.4.3/bowtie2-2.3.4.3-linux-x86_64.zip' -o /usr/local/bin/bowtie2-2.3.4.3.zip
    cd /usr/local/bin/ && unzip bowtie2-2.3.4.3.zip
    find /usr/local/bin/bowtie2-2.3.4.3-linux-x86_64 -type f -executable -exec ln -s {} /usr/local/bin \; 
    ## SPAdes
    curl -fsSL 'http://cab.spbu.ru/files/release3.13.0/SPAdes-3.13.0-Linux.tar.gz' | tar -xz -C /usr/local/bin/
    find /usr/local/bin/SPAdes* -name "spades.py" -type f -executable -exec ln -s {} /usr/local/bin \;


    ## CD-HIT
    curl -fsSL 'https://github.com/weizhongli/cdhit/releases/download/V4.6.8/cd-hit-v4.6.8-2017-1208-source.tar.gz' | tar -xz -C /usr/local/bin
    cd /usr/local/bin/cd-hit-v4.6.8-2017-1208 && make && make install

    pip3 install ariba

%runscript
    exec ariba "$@"