DEVELOPMENT.md

Installing a development version

Option 1) Installing the development version

You can install a development version from the github repository by using the devtools package. On windows Rtools needs to be installed on the system. So first download and install the version of Rtools that matches your current R version.

After installation of Rtools, run the following commands in the R terminal to download and install the CTL mapping package. Uncomment the first line (by removing the #), if you do not have devtools installed yet:

# install.packages("devtools")
library(devtools)                                         # Load the devtools package
install_github("DannyArends/CTLmapping", subdir="Rctl")   # Install the package from Github

After this learn more about the the R commands to start mapping CTLs on example data and how to prepare your own experimental data.

Option 2) Manually install the R source code

The second (more complex) option to is to clone the package from Github, this will give you access to the R source code and also allows you to build the standalone linux executables . On windows Rtools needs to be installed on your system. Download and install the version of Rtools that matches your current R version.

Prepare your environment by download and installing the R environment from www.r-project.org. Get the CTL mapping source code by download and afterwards 'move' into the folder:

git clone git://github.com/DannyArends/CTLmapping.git  # Download the repository
cd CTLmapping                                          # Goto the folder

The downloaded CTLmapping can be installed into R by using the following command (from a terminal / command line):

R CMD INSTALL Rctl                                     # Install the package

or use the 'installR' makefile target:

make installR                                          # Install into R