limix.def

Bootstrap: docker
#From: continuumio/miniconda3
From: continuumio/miniconda3:4.12.0
######################## Limix based QTL mapping ###########################
%runscript
    export PATH=/opt/conda/bin:${PATH}
    /bin/bash
%post
    export PATH=/opt/conda/bin:${PATH}
    git clone https://github.com/single-cell-genetics/limix_qtl.git
    # Initiate conda
    conda package
    conda config --add channels conda-forge
    # Install C & Python packages with conda.
    conda install -c conda-forge python=3.8 'blas=*=*mkl' 'numpy==1.21' pytest pytables scikit-learn matplotlib-venn bgen=4 pandas-plink

    # Install remaining Python packages with pip
    pip install --no-cache-dir h5py
    pip install bgen-reader
    pip install glimix-core
    # Install R
    apt-get update 
    apt-get -y install r-base
    # Install R packages (from within R)
    R --slave -e 'install.packages(c("BiocManager"))'
    R --slave -e 'BiocManager::install(c("qvalue","multtest","rhdf5","dplyr","readr"))'
##############################################################################