Bootstrap: docker
From: condaforge/mambaforge
IncludeCmd: yes

%files
env/binning.yml /

%post
# build-essential g++ are needed to pip install checkm2
apt-get update && apt-get install -y procps build-essential g++ && apt-get clean -y
/opt/conda/bin/mamba env create -q -f /binning.yml  && /opt/conda/bin/conda clean -a

export PATH=/opt/conda/envs/binning/bin:$PATH

# install Binette
wget  https://github.com/genotoul-bioinfo/Binette/archive/refs/tags/v0.1.5.tar.gz 
tar -xf v0.1.5.tar.gz 
rm v0.1.5.tar.gz

pip install Binette-0.1.5/

%environment
export PATH=/opt/conda/envs/binning/bin/:/checkm2/bin/:$PATH

%runscript
     "$@"
 

 
