singularity.kraken2_processing

BootStrap: docker
From: continuumio/miniconda3

%setup
    mkdir -p ${SINGULARITY_ROOTFS}/users

%environment
    PATH="/opt/conda/bin:$PATH"

%post 
    ln -s /bin/tar /bin/gtar
    export PATH=/opt/conda/bin:$PATH
    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc

    apt-get install -y libcurl3-dev gcc zlib1g-dev
    conda install -y -c conda-forge -c r -c bioconda r r-devtools r-ggplot2 r-ggpubr r-rcolorbrewer r-reshape2 r-vegan r-stringi r-devtools r-zcompositions r-compositions r-rafalib r-curl r-data.table bioconductor-flowcore 

    # install some other packages
    Rscript -e 'install.packages("RCurl", repos = "http://cran.us.r-project.org")'
    Rscript -e 'install.packages("matrixStats", repos = "http://cran.us.r-project.org")'
    Rscript -e 'install.packages("BiocManager", repos = "http://cran.us.r-project.org")'

    # get cmapR and dependencies
    Rscript -e 'devtools::install_github("grimbough/Rhdf5lib")'
    Rscript -e 'BiocManager::install("rhdf5")'
    Rscript -e 'BiocManager::install("prada")'
    Rscript -e 'BiocManager::install("SummarizedExperiment")'
    Rscript -e 'BiocManager::install("flowCore")'
    Rscript -e 'devtools::install_github("cmap/cmapR", dependencies = F)'

    # aldex2 and dependencies 
    Rscript -e 'BiocManager::install("GenomicRanges")'
    Rscript -e 'BiocManager::install("BiocParallel")'
    Rscript -e 'BiocManager::install("ALDEx2")'


    Rscript -e 'install.packages("stringi", repos = "http://cran.us.r-project.org")'
    # CoDaSeq functions
    # Rscript -e 'install.packages("car", repos = "http://cran.us.r-project.org")'
    # Rscript -e 'devtools::install_github("ggloor/CoDaSeq/CoDaSeq", dependencies = F)'

%runscript
   exec /bin/bash