Installation of msBayes for normal user (without root access).

It is easiest if you can ask your computer administrater to install all of the components for msBayes, but it may not be always possible. If you do not have root access to the computer, you should still be able to install msBayes and all required programs. Here we show you how to install everything in your home directory. Let's assume that your user ID is thomas, and your home directory is /home/thomas.

If you don't know the location of your home directory,

echo $HOME

will tell you where it is located.

Installation of R in your home directory.

R installation and Administration manual may be helpful.
  1. Download and unpack the R source code

    tar xvfz R-x.y.z.tar.gz

    with x.y.z replaced with the version number.

  2. Go inside of the unpacked source directory and compile

    cd R-x.y.z
    mkdir r-pkg
    ./configure --prefix=$HOME/r-pkg
    make
    make install

  3. The executable command of R is now installed in /home/thomas/r-pkg/bin/R. You need to add this directory to your PATH.

    cat 'PATH=$PATH:$HOME/r-pkg/bin' >> $HOME/.bash_profile source ~/.bash_profile

  4. Make sure you can find R.

    which R

    This should tell you /home/thomas/bin/r-pkg/bin/R. If it returns error message: /usr/bin/which: no R in ...., something went wrong.

Installation of GSL in your home directory

  1. Download and unpack the source code. tar xzvf gsl-x.y.tar.gz
  2. Compilation and installation

    cd gsl-x.y
    ./configure --prefix=$HOME/gsllib
    make
    make install

Installation of msBayes

Follow the section 2, "COMPILATION and INSTALLATION", of install direction. The only change you need to make in the instruction is to substitute

make clean; make

with

make LDFLAGS=-L$HOME/gsllib/lib/ -I$HOME/gsllib/include