BootStrap: docker
From: ubuntu:xenial

%help
    This singularity install hiddenDomains v3.1

%post

    # ~~~~~~ General setup and folder creation ~~~~~~ #
    
    apt-get update && apt-get install -y wget bzip2
    
    export LC_ALL=en_US.UTF-8
    export LC_COLLATE=C
    export LC_CTYPE=C
    export LC_MEASUREMENT=C
    export LC_MESSAGES=C
    export LC_MONETARY=C
    export LC_PAPER=C
    export LC_TIME=C
    export LANG=C.UTF-8
    
    # ~~~~~ MINICONDA 3.4.0.5 ~~~~~ #
    wget https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh && \
    bash Miniconda3-4.6.14-Linux-x86_64.sh -b -p /conda && \
    rm -f Miniconda3-4.6.14-Linux-x86_64.sh
    export PATH="/conda/bin:${PATH}"
    
    # ~~~~~ perl 5.32.1 ~~~~~~~#
    conda install -c conda-forge perl=5.32.1
    
    # ~~~~ R v 4.1.2 ~~~~~~ #
    conda install -c conda-forge r-base=4.1.2
    
    # ~~~ r-depmixs4 v1.5_0 ~~~~#
    conda install -c conda-forge r-depmixs4=1.5_0
    
    #~~~~ r-hiddenmarkov v1.8_13 ~~~#
    conda install -c conda-forge r-hiddenmarkov=1.8_13
    
    # ~~~~~ hiddendomains v3.1 ~~~~~ #
    conda install -y -c bioconda hiddendomains=3.1
    
%environment
    export PATH="${PATH}:/conda/bin"
    export LC_ALL=en_US.UTF-8
    export LC_COLLATE=C
    export LC_CTYPE=C
    export LC_MEASUREMENT=C
    export LC_MESSAGES=C
    export LC_MONETARY=C
    export LC_PAPER=C
    export LC_TIME=C
    export LANG=C.UTF-8
    

%labels
    Author Nicolas Descostes
    Version v0.0.5