WOMBAT – A program for Mixed Model Analyses by Restricted Maximum Likelihood

Table of Contents

Linux

Installation

  1. Download the appropriate, pre-compiled executable program for your computer. Unless you have an old or `unusual' machine, this should be
  2. Screenshot 1

    Say you want to keep your WOMBAT in the directory MyPrograms and that you have moved the file you downloaded to this directory.
    The screen-shots show this for wombat64 but the procedure is analogous for wombat32. They show MyPrograms as a sub-directory of my home directory – this is not a necessary requirement; for instance, if you have super-user privileges, you may want to choose something like /usr/local instead.

    • Change into your selected directory:
      cd MyPrograms
    • Create a new directory called WOMBAT:
      mkdir WOMBAT
    • Check that your downloaded file and new directory are there:
      ls -l

      should give you something like shown on the right, but, of course, with different names and date.

  3. Unpack your file into the new directory.

    • Change into directory WOMBAT:
      cd WOMBAT
    • Unpack the file – the extension .tar.gz tells you that this is a gzipped tar file. Hence the command is
      tar -zxvf ../wombat64.tar.gz

      This will create a single file wombat.

    • To check that it is there:
      ls -l
    • The file properties should be –rwx–x–x with the three x signifying that this program is executable by anybody. If these are missing for any reason, try:
      chmod a+x wombat

      followed by ls -l to see the change.

  4. To run the program from any directory, you need to give it the full path name, i.e. in this case
    /home/kmeyer/MyPrograms/WOMBAT/wombat

    This can get a bit tedious to make live simpler – so that you can run the program by simply typing wombat – either:

    1. add your equivalent to /home/kmeyer/MyPrograms/WOMBAT to the PATH statement in the file which is executed whenever you login or start a new shell.
      • If you are using the bash shell, this is .bashrc or similar
      • If you are using the csh or tcsh, this is .cshrc_usr (ubuntu) or similar; look for the set path statement
         set path = (.:${HOME}/bin:/usr/local/bin:/usr/bin:$path)

        and append the new directory to be searched. In this example, it is ''/home/kmeyer/MyPrograms/WOMBAT'' or, equivalently ''${HOME}/MyPrograms/WOMBAT''

         set path = (.:${HOME}/bin:/usr/local/bin:/usr/bin:${HOME}/MyPrograms/WOMBAT: $path)
    2. Create a symbolic link to the program from a directory which is already in your search path. For example,
      cd /usr/local/bin
      ln -s /home/kmeyer/MyPrograms/WOMBAT/wombat wombat

      You may need super-user or administrator privileges to do so. For all three alternatives, you may need to log off and back on again (or start a new shell) before the new setting becomes effective.

    3. Move the program file to a directory which is in your search path.
  5. Larger analyses in WOMBAT may require more than the default stack size set in your flavour of Linux. If you are planning to run large models, it is a good idea to set the stack size to as large as possible in your .login (or .bashrc or .cshrc_usr) file, e.g. ulimit -s

Testing

To test your installation, it is highly recommended that you run one or more of the examples provided.

  1. Download an example of your choice, e.g. example1.tar.gz
  2. Move this this tar file into MyPrograms/WOMBAT (or another directory of your choice).
  3. Unpack the example:
    tar -zxvf example1.tar.gz

    This will create the directory Examples with subdirectory Example1.

  4. Change into a subdirectory
    cd Examples/Example1/A
  5. For example 1, the parameter file is wombat.par. This is the default, WOMBAT will look for it if no other name is given. Hence you can run the example by simply typing
    wombat

    (if you have followed the steps above to be able to do so) or, equivalently, by typing

    /home/kmeyer/MyPrograms/WOMBAT/wombat

    The screenshot below shows the output to the screen you should get.

More examples

Other small examples to try are:

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