tombo(1).def

Bootstrap: library
From: ubuntu:22.04

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

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

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


	usage (help)	: singularity run tombo.sif
	usage (basic)	: 1 st step : conda activate tombo 
			  2 nd step : tombo [option] 
	
	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

	apt-get install -y libc6
	
	
    # ================================
    # 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
	apt-get install -y git-all
	
	# Conda Environement Creation
	
	
	conda create --name tombo python=3.7
	. activate tombo
	pip install numpy==1.19.4
	git clone https://github.com/nanoporetech/tombo
	cd tombo
	pip install -e .
	
	
%labels 	
	TOMBO-ONT