Installation

3.1 Installation

WOMBAT is distributed currently only as a pre-compiled executable file¹. Installation instructions below are for LINUX operating systems (including CYGWIN under WINDOWS). Versions for 32-bit and 64-bit personal computers are available.

Installation is simple :

1. Download the version appropriate to your machine from
http://agbu.une.edu.au/ $∼$ kmeyer/wombat.html

wombat32.tar.gz for standard 32-bit PCs
wombat64.tar.gz for 64-bit PCs
wombatwin.tar.gz for 32-bit PCs emulating a LINUX environment under Windows through CYGWIN

2. Uncompress and unpack the file ( $nn = 32$ or $64$ or win) using
tar -zxvf wombat $nn$ .tar.gz
This will create the directory WOMBAT which contains the executable wombat.
3. Check that your system recognises wombat as an executable file (e.g. using ls -l WOMBAT/wombat).
If necessary, use the chmod command to add executable permission or access permission for other users (e.g. chmod a+x WOMBAT/wombat).
4. Make sure that the system can find WOMBAT, by doing one of the following :

Add WOMBAT to your PATH statement, or
Move wombat to a directory which is included in your PATH, e.g. /usr/local/bin (this requires super-user privileges) or $∼$ /bin in your home directory, or
Make a symbolic link from a bin directory to WOMBAT/wombat (using ln -s).

HINT: PATH is set in your login file, e.g. .login_usr, or shell start-up file, e.g. .tcshrc; use printenv PATH to check your current PATH settings.

Done !

3.1.1 Examples and testing

A number of worked examples, complete with output files and captured screen output, are provided; see chapter 9 for further details. These can be downloaded and installed in analogous manner to the program.

1. Download examples.tar.gz from
http://agbu.une.edu.au/ $∼$ kmeyer/wombat.html
2. Uncompress and unpack the file using
tar -zxvf examples.tar.gz
Do this in the same directory as above ! This will create the directory WOMBAT/Examples with subdirectories Example1, $...$ , Example $n$ .

Each subdirectory contains the input and output files for a run of WOMBAT, together with a records of the screen output in the file typescript. To test your installation,

1. Choose an example and change into its directory.
2. Make a new temporary subdirectory, e.g. try.

N.B.: This should be a ‘parallel’ directory to sub-directories A,B, $...$ , i.e. Example $n$ /try not Example $n$ /A/try. Qtherwise, you need to adjust the paths to the data and pedigree files in the parameter file for WOMBAT to be able to find them !

3. Copy all input files to the temporary directory.
4. Change into the temporary directory and run WOMBAT, using the same command line options (if any) as shown in the beginning of typescript.
5. Compare your output files with those supplied – apart from date and time they should be virtually identical; small discrepancies in higher decimals may occur though.
6. Delete temporary subdirectory.

Repeat for at least one more example.

3.1.2 Compilation notes

The LINUX versions of WOMBAT have been compiled under Fedora Core 5, using the Pathscale Ekopath™ FORTRAN 95 compiler, version 2.2.1. The 32 bit and 64 bit versions have been optimised for Pentium 4 and AMD Opteron processors, respectively. The additional 32 bit LINUX versions (for debugging or older machines and LINUX versions) have been compiled using the Lahey™ LF95 compiler (version 6.20c) under Fedora Core 2. Compiled programs have been tested under Fedora Core 2 to 5, as well as Ubuntu 7.04.

The WINDOWS versions of WOMBAT have been compiled using the g95 FORTRAN compiler. Execution times for programs generated with this free compiler (available from http://www.g95.org) tend to be slower than those produced by commercial compilers. Programs have been compiled both under CYGWIN and under MINGW. These versions of WOMBAT are primarily intended for evaluation and teaching purposes. Hence, the executables have been restricted to smaller analyses, allowing for models with a maximum of $150000$ equations and at most $50000$ animals in the analysis.

3.1.3 Updates

WOMBAT is set up to ‘expire’ after a certain date. Usually this is the end of the calendar year.² This feature aims at reducing the number of outdated copies being used, and any associated problems. WOMBAT will print out a warning message when used in the month preceding the expiry date. In addition, a run time option is available to query the program for this date.

If your copy of WOMBAT has expired – or you simply want to update to a newer version, please repeat the installation steps outlined above (section 3.1).

¹“Open Source” to be considered later

²At present, during active development, WOMBAT may only be ‘valid’ for a few months

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