mapDamage

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')