deepmp.def

Bootstrap: library
From: ubuntu:18.04

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

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

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


	usage (help)	: singularity run deepmp.sif
	
	building container : singularity build deepmp.sif deepmp.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}
     apt-get install -y git
    # ================================
    # 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
	export PATH=$PATH:/usr/local/bin/conda
    # ===============================
    # INSTALL DeepMP
    # ===============================
	git clone https://github.com/pepebonet/DeepMP.git
	conda create --name deepmp_2021 python=3.8
	#conda activate 
	#conda deactivate 
	#conda activate deepmp_2021
	#cd ..
	cd DeepMP
	pip install -e .
	pip install numpy
	pip install ont-tombo
	pip install biopython
	conda install -c bioconda samtools
	conda install -c bioconda minimap2
	conda install -c anaconda openjdk
	conda install -c anaconda bottleneck
	pip install numpy --upgrade