Singularity.spikchipcustom-v099

BootStrap: docker
From: ubuntu:22.10


%help

    This singularity installs spikchip. See repository https://github.com/eblancoga/spikChIP

%post
    # ~~~~~~ General setup and folder creation ~~~~~~ #
    
    apt update && DEBIAN_FRONTEND=noninteractive apt install -y gcc git libz-dev make r-base curl samtools software-properties-common gawk bash
    
    export LC_ALL=C
    export LC_CTYPE=C 
    export LC_COLLATE=C 
    export LC_TIME=C
    export LC_MESSAGES=C
    export LC_MONETARY=C
    export LC_PAPER=C 
    export LC_MEASUREMENT=C
    
    # ~~~~~ seqcode ~~~~~ #
    curl -L https://github.com/eblancoga/seqcode/archive/master.tar.gz -o seqcode.tar.gz && tar -xvzf seqcode.tar.gz && rm seqcode.tar.gz && cd seqcode-main/ && make all && cd ..
    
    # ~~~~~ samtools ~~~~~ #
    add-apt-repository universe && apt update && apt install -y samtools
    
    # ~~~~~ affy and MASS ~~~~~ #
    R --slave -e 'install.packages(c("BiocManager", "MASS"), repos="https://cloud.r-project.org/")' && R --slave -e 'BiocManager::install(c("affy"))'
    
    # ~~~~~ spikchip ~~~~~ #
    curl -L https://github.com/descostesn/spikChIP/archive/overwrite.tar.gz -o spikchip.tar.gz && tar -xvzf spikchip.tar.gz && rm spikchip.tar.gz && cd spikChIP-overwrite/ && rm -r examples && cd ..
    
%environment
    export PATH="${PATH}:/spikChIP-overwrite:/seqcode-main/bin"
    export LC_ALL=C
    export LC_CTYPE=C 
    export LC_COLLATE=C 
    export LC_TIME=C
    export LC_MESSAGES=C
    export LC_MONETARY=C
    export LC_PAPER=C 
    export LC_MEASUREMENT=C

%labels
    Author Nicolas Descostes
    Version v0.0.1