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INSTALL.md

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TractoR consists of several R packages and a set of other files which provide an interface to key functions within those packages. The interface requires a "bash" shell, and is therefore only designed to work on Unix-like operating systems, such as Linux or Mac OS X. In particular, it will not work directly on Windows, and Windows users are therefore recommended to run Linux within a virtual machine, and then install TractoR (and R) within that virtual environment. The virtual machine image provided by the FSL package is one suitable example.

Quick installation for knowledgeable users

  1. Install R if necessary. See http://www.r-project.org.

  2. Open a terminal, navigate to the uncompressed "tractor" directory and type make install. A C/C++ compiler must be available and known to R.

  3. Create or update the TRACTOR_HOME environment variable to point to the "tractor" directory, include ${TRACTOR_HOME}/bin on the PATH and ${TRACTOR_HOME}/share/man on the MANPATH.

  4. Consider installing FSL, if it is not already installed. It is used by some elements of TractoR's functionality.

Details and step-by-step explanation

Before installing TractoR, R must be installed. R runs on almost all platforms and is simple to install. It can be obtained from http://www.r-project.org.

A C/C++ compiler is also required to build parts of the package. A suitable compiler can be installed using an appropriate package manager (aptitude, yum, etc.) on Linux, or with Xcode (from the Mac App Store) on OS X. R handles all the details of actually compiling code.

Once R and the C/C++ compiler are installed, the TractoR R packages can be installed by opening a terminal window and running

make install

from the uncompressed "tractor" directory. To test that the installation was successful, type

make clean test

and a series of standard tests will be run.

For the "tractor" interface to function correctly, the TRACTOR_HOME and PATH environment variables should be set appropriately. To do this, add the following lines to your ~/.bashrc (or equivalent for other shells):

export TRACTOR_HOME=/usr/local/tractor
export PATH=${TRACTOR_HOME}/bin:${PATH}
export MANPATH=${TRACTOR_HOME}/share/man:${MANPATH}

(Note that the first line may need to be modified to reflect the actual location of the uncompressed "tractor" directory on your system. You should get a prompt giving the appropriate lines for your case after running make install above.) To make sure that "login" shells also pick up these variables, you may also wish to point your ~/.bash_profile at ~/.bashrc. This can be achieved with the line

[ -f ~/.bashrc ] && source ~/.bashrc

in ~/.bash_profile (create this file if it doesn't exist). To check that everything is functioning correctly, you can try the following commands after opening a new terminal window:

cat ${TRACTOR_HOME}/VERSION   # should print the current TractoR version
man tractor                   # should open the "tractor" man page
tractor list                  # should list the TractoR scripts installed

For further information on using the TractoR interface, type tractor -h or take a look at the man page. To find out what a particular script does, type tractor -o (script_name), replacing (script_name) with the name of the script you are interested in.

Finally, you may want to consider also installing FSL, if it is not already installed. It is used by some elements of TractoR's functionality, so installing it now will avoid any problems with missing software later.