Singularity.cleanfastq

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


%environment    
	export LC_ALL=C.UTF-8
	export PATH="${PATH}":/usr/local/bin/bbmap/

%runscript
    echo "Opening container...ubuntu xenial: fastq_illumina_filter, bbduck, fastp"


%labels
    MAINTAINER Pierre-Edouard_GUERIN
    INSTITUTE CNRS
    TEAM Biogeographie_Ecologie_Vertebres
    BUILD 1.2
    SINGULARITY_VERSION 2.4.2-dist
    JAVA 8.0
    fastp 0.20.0
    bbduck 1.0
    fastq_illumina_filter 0.1



%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 install wget
    yes | apt-get install autoconf autogen libtool

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

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

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

    ## illumina casava filter
    wget http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/release/0.1/fastq_illumina_filter-0.1.tar.gz
    tar -xzf fastq_illumina_filter-0.1.tar.gz
    cd fastq_illumina_filter-0.1
    make
    chmod +x fastq_illumina_filter
    cp fastq_illumina_filter /usr/local/bin
    cd ..

	## remove phiX
	wget 'https://sourceforge.net/projects/bbmap/files/BBMap_38.57.tar.gz'
	tar xvzf BBMap_38.57.tar.gz
	chmod 777 -R bbmap
    cp -R bbmap/ /usr/local/bin/