meekrob/RSummit_container:latest

$ singularity pull shub://meekrob/RSummit_container:latest

Singularity Recipe

BootStrap: docker
From: ubuntu:16.04

%post

    # install some system deps
    apt-get -y update
    apt-get -y install locales curl bzip2 less unzip git wget vim ant default-jdk
    # this is a X11 dep 
    apt-get -y install libxext6
    # tools to open PDF and HTML files
    apt-get -y install firefox xpdf
    # some extra devel libs
    apt-get -y install zlib1g-dev libssl-dev libpng-dev uuid-dev
    # other
    locale-gen en_US.UTF-8
    apt-get clean

    # download and install miniconda3
    curl -sSL -O https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
    bash Miniconda3-latest-Linux-x86_64.sh -p /opt/miniconda3 -b
    rm -fr Miniconda3-latest-Linux-x86_64.sh
    export PATH=/opt/miniconda3/bin:$PATH
    conda update -n base conda
    conda config --add channels conda-forge
    conda config --add channels bioconda

    # install the R programming language
    conda install --yes -c conda-forge r-base==3.5.1

    # install some dependencies to build R packages
    apt-get -y install build-essential gfortran

    # install R bioconductor including DESeq2
    Rscript -e "install.packages('BiocManager', repos='https://cran.rstudio.com'); BiocManager::install('ggtree')"
    Rscript -e "source ('https://bioconductor.org/biocLite.R'); biocLite(c('ape', 'pegas', 'adegenet', 'ChIPpeakAnno','phangorn', 'sqldf', 'ggplot2', 'ggExtra', 'phytools', 'DESeq2','monocle', 'edgeR','ShortRead','rtracklayer','GenomicFeatures','Rsamtools','biomaRt','Repitools','QuasR'))"

    # install fastp
    wget http://opengene.org/fastp/fastp -P /opt/bin/
    chmod a+x /opt/bin/fastp
    export PATH="/opt/bin:$PATH"

%environment
    export LANG=en_US.UTF-8
    export LANGUAGE=en_US:en
    export LC_ALL=en_US.UTF-8
    export XDG_RUNTIME_DIR=""
    export PATH=/opt/miniconda3/bin:$PATH
    export PATH=/opt/bin/fastp:$PATH

Collection

• Name: meekrob/RSummit_container
• License: None

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