bio tools

install.def

BootStrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/


%runscript
    echo "This is what happens when you run the container..."


%post
    echo "Hello from inside the container"
    sed -i 's/$/ universe/' /etc/apt/sources.list

    apt-get -y update
    apt-get -y upgrade
    apt-get -y dist-upgrade

    apt-get install cmake -y
    apt-get update; 
    apt-get install -y software-properties-common
    #apt-get install add-apt-repository
    apt-get update
    apt-get install git -y
    apt-get install libboost-all-dev -y 

    apt-get update && apt-get install -y linux-tools-generic
    apt-get install wget curl

    #Python3.6 and pip
    add-apt-repository ppa:deadsnakes/ppa  
    apt-get update && apt install python3.6 -y
    #curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
    #python3.6 get-pip.py
    apt-get update
    apt-get -y install python3-pip
    pip3 --version

    pip3 install Cython

    #pip3 install whatshap
    #export PATH=$HOME/.local/bin:$PATH
    #cp /root/.local/bin/whatshap /usr/local/bin/
    #chmod +x /usr/local/bin/whatshap
    #apt-get -y update
    #whatshap --help


    #pip3 install pyarrow==3.0.0
    apt-get install -y libbz2-dev
    apt-get install -y liblzma-dev
    apt-get install -y libncurses5-dev

    pip3 install pysam
    pip3 install pandas
    pip3 install numpy

    apt-get install tabix

    apt-get install -y dh-autoreconf

    git clone https://github.com/samtools/htslib.git
    cd htslib/
    git submodule update --init --recursive
    autoreconf -i
    ./configure
    make
    make install
    cd ..

    wget https://github.com/samtools/samtools/releases/download/1.12/samtools-1.12.tar.bz2
    tar -xvjf samtools-1.12.tar.bz2 
    cd samtools-1.12/
    ./configure #--prefix=/usr/local/bin/
    make
    make install
    #samtools
    cd ..

    #git clone git://github.com/samtools/bcftools.git
    #cd bcftools/
    #make
    #make install
    ##bcftools --help
    #cd ..

    git clone https://github.com/lh3/bwa.git
    cd bwa; make
    #make install
    cp bwa /usr/local/bin/
    #./bwa index ref.fa
    #./bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz
    #./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz
    cd ..

    git clone https://github.com/lh3/minimap2
    cd minimap2 && make
    #make install 
    cp minimap2 /usr/local/bin/
    cd ..
   
    apt-get -y update
    apt-get clean

%environment
    export PATH=$PATH:/usr/local/bin