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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