Singularity.methylkit

Bootstrap: shub
From: thakk/bioinformatics

%setup

%files

%help

   A container with R, Bioconductor and MethylKit installed on top of basic bioinformatics tools. For complete list see documentation of shub://thakk/bioinformatics

%labels
   Author francesco.tabaro@tuni.fi
   Version 0.1

%post

  dnf -y makecache

  # INSTALL DEPS
  dnf -y install --allowerasing bzip2 cairo fontconfig freetype fribidi glib2 \
    libX11 libXext libXt libcurl libicu libjpeg libpng libtiff libtirpc libxcrypt \
    ncurses pango pcre readline tcl tk xz zlib bzip2-devel cairo-devel \
    fontconfig-devel freetype-devel fribidi-devel glib2-devel libX11-devel \
    libXext-devel libXt-devel libcurl-devel libicu-devel libjpeg-devel libpng-devel \
    libtiff-devel libtirpc-devel libxcrypt-devel ncurses-devel pango-devel \
    pcre-devel readline-devel tcl-devel tk-devel xz-devel zlib-devel \
    java-1.8.0-openjdk java-1.8.0-openjdk-devel openblas lapack \
    gcc-gfortran boost boost-devel texlive

  # INSTALL R
  wget https://cran.rstudio.com/src/base/R-3/R-3.6.1.tar.gz
  tar xf R-3.6.1.tar.gz
  cd R-3.6.1
  ./configure
  make -j 8
  make install
  cd ..
  rm -r R-3.6.1

  # INSTALL Bioconductor
  R -e "install.packages('BiocManager', repos = 'https://cloud.r-project.org')"

  # INSTALL methylKit
  R -e "library(BiocManager); install('methylKit')"