Bootstrap: library
From: ubuntu:18.04

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

%help 

This container launches megalodon software used for the identification of modified nucleotides from nanopore sequencing data.

======================================================================================


	usage (help)	: singularity run megalodon.sif
	
	building container : singularity build tombo.sif tombo.def 


======================================================================================
%post
    # ================================
    # PREPARE the system
    # ================================
    export DEBIAN_FRONTEND=noninteractive
    apt-get update
    apt-get install -y software-properties-common
    apt-add-repository universe
    apt-get update
    export LC_ALL=C.UTF-8
    export LANG=C.UTF-8
    echo 'export LC_ALL=C.UTF-8' >> "$SINGULARITY_ENVIRONMENT"
    echo 'export LANG=C.UTF-8' >> "$SINGULARITY_ENVIRONMENT"

    apt-get install -y \
        wget \
        build-essential

    libboostVERSION="1.62.0"
    apt-get install -y \
        libidn11 \
        libidn11-dev \
        libgssapi-krb5-2 \
        libboost-atomic${libboostVERSION} \
        libboost-chrono${libboostVERSION}  \
        libboost-date-time${libboostVERSION} \
        libboost-filesystem${libboostVERSION} \
        libboost-program-options${libboostVERSION} \
        libboost-regex${libboostVERSION} \
        libboost-system${libboostVERSION} \
        libboost-log${libboostVERSION}
        
    # ================================
    # INSTALL python3.8
    # ================================ 

	apt-get -y install software-properties-common
	add-apt-repository ppa:deadsnakes/ppa
	apt-get -y install python3.8-distutils
	apt-get -y install python3.8
	ln -s /usr/bin/python3.8 /usr/bin/python
    # ================================
    # INSTALL guppy-cpu
    # ================================

    VERSION="6.0.1"
    URL="https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_6.0.1_linux64.tar.gz"
    wget "$URL" -O - | tar xzf -
    cd ont-guppy-cpu || exit 1
    for binary in bin/guppy_*
    do
        ln -s "$(realpath "$binary")" "/usr/local/bin/$(basename "$binary")"
    done

    # ================================
    # INSTALL conda	
    # ================================

	wget -c https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh
	/bin/bash Anaconda3-2020.02-Linux-x86_64.sh -bfp /usr/local
	#Conda configuration of channels from .condarc file
	conda config --file /.condarc --add channels defaults
	conda config --file /.condarc --add channels conda-forge
	conda update conda
	
	##Install Guppy 
	    VERSION="6.0.1"
    URL="https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_6.0.1_linux64.tar.gz"
    wget "$URL" -O - | tar xzf -
    cd ont-guppy-cpu || exit 1
    for binary in bin/guppy_*
    do
        ln -s -f "$(realpath "$binary")" "/usr/local/bin/$(basename "$binary")"
    done 
    pip install ont-pyguppy-client-lib==6.0.1
    # ================================
    # INSTALL MEGALODON
    # ================================
	
	pip install megalodon