mapDamage

mapDamage: tracking and quantifying damage patterns in ancient DNA sequences

View project onGitHub

Fresh installation on Mac OS using MacPorts

Tutorial written by Julien Soubrier and Bastien Llamas, tested on MacOS version 10.8.5.

  1. Install git:
    Follow the instructions available at git (with installers/packages available for all major operating systems).

  2. Install mapDamage:
    Clone the repository from GitHub
    git clone https://github.com/ginolhac/mapDamage.git mapDamage
    go into the resulting folder
    cd mapDamage
    then clone the submodules.
    git submodule update --init

    Continue the procedure by running the following command if you have administrator rights
    sudo python setup.py install
    otherwise install it locally
    python setup.py install --user
    then, $HOME/.local/bin must be in your PATH.

  3. Install Cython:
    Download the tarball archive for Cython.
    Untar the downloaded tar file and follow instructions in the INSTALL text file. The following should do:
    sudo python setup.py install

  4. Install pysam 0.6:
    Download the tarball archive for pysam.
    Untar the downloaded tar file and then
    sudo su
    export CC=llvm-gcc-4.2
    export CXX=llvm-g++-4.21
    python setup.py build
    sudo python setup.py install

  5. Install R:
    Follow the instructions available at R project (with installers/packages available for all major operating systems). Or use MacPorts:
    sudo port install r

  6. Install the R packages:
    By running in a R console and selecting a CRAN mirror:
    install.packages("inline")
    install.packages("gam")
    install.packages("Rcpp")
    install.packages("ggplot2")

  7. Install the GSL library gsl:
    Follow the instructions available at gsl website or using MacPorts:
    sudo port install gsl

  8. Install RcppGSL:
    In a R session do the following
    install.packages("RcppGSL", repos='http://cran.us.r-project.org')
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