snakePipes.def

BootStrap: docker
From: ubuntu:22.04
Stage: build

%help
This is a singularity container packing the snakePipes pipeline in version 2.5.3 and all the dedicated environnement set up for proper usage of the pipeline
Author : marine.bergot@u-bourgogne.fr
Bionano Solve pipeline is the property of Bionano Genomics Inc. All Rights Reserved

Launching a complete assembly could be perform with this command :

singularity exec -e snakePipes.sif \
hicexplorer command

exemple : 

singularity exec -e snakePipes.sif HiC --help


%environment

DEBIAN_FRONTEND=noninteractive


%post

apt-get update && apt-get -y upgrade
apt-get -y install build-essential wget bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 git
apt-get clean


# install python3.9
apt-get -y install python3.9
apt-get -y install build-essential zlib1g-dev libncurses5-dev libgdbm-dev libnss3-dev libssl-dev libreadline-dev libffi-dev wget


#Installing Miniconda 3 
wget -c https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh
bash Miniconda3-py39_4.12.0-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
#List installed environments
conda list



conda install -c mpi-ie -c bioconda -c conda-forge snakePipes


%labels
Maintainer Marine Bergot
Updater Marine Bergot <marine.bergot@u-bourgogne.fr>
ContainerVersion v0.1
snakePipes pipeline v2.5.3

%runscript
echo "OK"