Singularity.seaconnect

BootStrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
IncludeCmd: yes
Include: bash vim less man-db apt-utils tzdata


%environment
    PATH="${PATH}":/usr/local/bin/bin/    

%runscript
    echo "Opening container...ubuntu xenial: freebayes, STACKS1, dDocent, DEMORT, parallel, gnuplot, mawk, VCFtools, VCFlib, trimmomatic, bwa, CD-HIT, samtools, bedtools, PEAR, fastp, seqtk, curl, wget, python2, java8"


%labels
    MAINTAINER Pierre-Edouard_GUERIN
    INSTITUTE CNRS
    TEAM Biogeographie_Ecologie_Vertebres
    BUILD 1.0
    SINGULARITY_VERSION 2.4.2-dist
    curl 7.47.0
    Python 2.7.12
    freebayes 1.3.1
    STACKS 1.48
    CD-HIT 4.6
    samtools 1.3.1
    bedtools 2.26.0
    PEAR 0.9.11
    fastp 0.20.0
    dDocent 2.7.6
    VCFtools 0.1.14
    Trimmomatic 0.33
    JAVA 8.0    
    GNUPLOT 5.0
    MAWK 1.2
    rainbow 2.0.4
    parallel 20161222
    seqtk 1.0
    BWA 0.7.17
    DEMORT 0.2.4


%post
    mv /etc/apt/sources.list /etc/apt/sources.list.bak

    echo "deb http://us.archive.ubuntu.com/ubuntu/ xenial main restricted universe multiverse
    deb-src http://us.archive.ubuntu.com/ubuntu/ xenial main restricted universe multiverse
    deb http://us.archive.ubuntu.com/ubuntu/ xenial-security main restricted universe multiverse
    deb http://us.archive.ubuntu.com/ubuntu/ xenial-updates main restricted universe multiverse
    deb http://us.archive.ubuntu.com/ubuntu/ xenial-proposed main restricted universe multiverse
    deb http://us.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse
    deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-security main restricted universe multiverse
    deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-updates main restricted universe multiverse
    deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-proposed main restricted universe multiverse
    deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse" >> /etc/apt/sources.list


    ## git, make, wget
    apt-get -y --force-yes update
    yes | apt-get install build-essential
    yes | apt-get install git
    yes | apt-get install wget
    yes | apt-get install autoconf autogen libtool

    ## zlib, cmake
    yes | apt-get install zlib1g-dev libbz2-dev pkg-config cmake

    ## curl, lzma
    yes | apt-get install curl liblzma-dev libncurses5-dev

    ## python2 minimal
    yes | apt-get install python-minimal

    ## lib-python
    yes | apt-get install libpython-dev unzip bc

    ## python3 minimal
    yes | apt-get install python3

    ## DEMORT
    yes | apt-get install python3-pip
    python3 -m pip install --upgrade pip==9.0.3
    pip3 install demort 
    yes | apt-get install python3-tk


    ## install STACKS    
    wget http://catchenlab.life.illinois.edu/stacks/source/stacks-1.48.tar.gz
    tar -xvzf stacks-1.48.tar.gz
    cd stacks-1.48
    ./configure --prefix=/usr/local/bin
    make
    make install
    cd ..    

    ## freebayes
    git clone --recursive https://github.com/ekg/freebayes.git
    cd freebayes
    make
    cd bin
    chmod +x *
    cp -f * /usr/local/bin
    cd ..
    cd ./vcflib/
    make
    chmod +x ./bin/*
    cp -f ./bin/* /usr/local/bin
    cd ../..

    ## JAVA
    yes | apt-get install openjdk-8-jdk

    ## trimmomatic
    curl -O http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip
    yes | unzip Trimmomatic-0.33.zip
    cd Trimmomatic-0.33
    cp -f ./adapters/* /usr/local/bin
    cp -f trimmomatic-0.33.jar /usr/local/bin
    cd ..

    ## mawk, gnuplot, parallel
    yes | apt-get install mawk gnuplot parallel

    ## bwa
    git clone https://github.com/lh3/bwa.git
    cd bwa
    make
    chmod +x bwa
    cp -f bwa /usr/local/bin
    cd ..

    ## PEAR
    wget https://github.com/Grelot/bioinfo_singularity_recipes/raw/master/packages/pear-0.9.11-linux-x86_64.tar.gz
    tar xzf pear-0.9.11-linux-x86_64.tar.gz
    cp pear-0.9.11-linux-x86_64/bin/pear /usr/local/bin/pearRM

    ## FASTP
    git clone https://github.com/OpenGene/fastp.git
    cd fastp
    make && make install
    cd ..

    ## dDocent samtools bamtools CD-HIT rainbow seqtk bedtools
    wget https://github.com/jpuritz/dDocent/archive/v2.7.6.tar.gz
    tar -xvzf v2.7.6.tar.gz
    cd dDocent-2.7.6
    bash install_dDocent_requirements /usr/local/bin/