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WOMBAT meets Cygwin

What is Cygwin ?

• Cygwin is a Windows program which emulates a Linux environment.
• Running Cygwin opens a window in which you can execute other programs, compiled for this environment.
• In principle, this is very similar to opening a DOS window and running a program in it. The main difference is that a number of Linux utilities are available as well. In addition, paths and filenames are specified using a forewards (/) rather than a backwards (\) slash !
• If all you want to do is run WOMBAT, you can get away with learning just a few basic Linux commands.

How to install Cygwin

• Cygwin is is avalaible (free of charge) from www.cygwin.com.
• Installing Cygwin is as simple as downloading a 'setup.exe' program, double-clicking on it and following the instructions. Only the default packages are needed to run WOMBAT.
• During the set-up steps :
  1. Make a note of the install directory. The default is C:\cygwin. This is assumed in the following; if you choose a different name, please substitute it below when C:\cygwin is referred to.
  2. When offered a choice of packages to install, click on 'base' and make sure that 'gzip' is selected.
  3. If you want to edit files (e.g. the parameter file for WOMBAT) under Cygwin, click on 'editors' and select an editor to install.
  4. Choose to install a Cygwin icon on your Desktop when given the choice.
• There are various detailed tutorials (including step-by-step screenshots) available on the web. For example :
  • bioinformatics.ubc.ca/resources/tutorials/installing_cygwin_x
  • www.physionet.org/physiotools/cygwin/
  • www.mobilefish.com/developer/cygwin/cygwin.php

Getting started with WOMBAT

1. Download wombatwin.tar.gz and examples.tar.gz from the WOMBAT homepage.
2. Under Windows, open the folder C:\cywin. You should see various folders in it named bin, etc, home, lib, etc.
3. Open home. In it, you should find a folder usern, where 'usern' is your windows user name.
4. Open usern. It should be empty, except for some so-called dotfiles, .bashrc and .bash_profile.
5. Move (or copy) both wombatwin.tar.gz and examples.tar.gz into usern.
6. Double click on the Cygwin icon on your desktop. This opens the Cygwin window.
7. At the prompt, type the command pwd (short for 'print working directory'). The answer should be /home/usern. This is the name under which Cygwin knows C:\cygwin\home\usern i.e. opening Cygwin automatically puts you into your home directory. Issue the command ls -lf to list the contents of the directory. The answer should include wombatwin.tar.gz and examples.tar.gz.
8. You are now ready to unpack the two files, as detailed in the WOMBAT User Notes, chapter 3.
   1. Issue the command : tar -zxvf wombatwin.tar.gz
   2. Issue the command : tar -zxvf examples.tar.gz
   This will create the directory (folder) WOMBAT in /home/usern.
9. Change into this directory by issueing the command: cd WOMBAT
   See what is in the directory using the command: ls -lf
   You should have a file wombat.exe and a subdirectory Examples.
10. Run your first test as follows :
    1. Change directory with the command : cd Examples/Example1/A
    2. Run WOMBAT with the command : /home/usr/WOMBAT/wombat.exe
11. To avoid typing the long path /home/usr/WOMBAT/ in the future, move (or copy) wombat.exe to /usr/local/bin. The Linux command to do this is mv wombat.exe /usr/local/bin . Alternatively, you can do this under windows.
    This is a directory which is searched automatically for executable files (however, this won't take effect until the next time you open the Cygwin window).
    Close the Cygwin window (or type logout at the command prompt).
12. Re-open Cygwin. Run your second test example as follows :
    1. Change directory with the command : cd WOMBAT/Examples/Example2/A
    2. Run WOMBAT with the command : ./wombat.exe

Compilation notes for WOMBAT

• The Cygwin version of WOMBAT has been compiled with the free 'g95' compiler (available from www.g95.org).
  While this compiler is a wonderful resource, it tends to produce executable programs with somewhat slower run times than some of the commercial compilers available. This is of little consequence for small to medium sized analyses - for larger scale analyses, however, we recommend that you switch to Linux proper and a faster version of WOMBAT.
• Hence, the Cygwin version of WOMBAT is meant primarily as a demonstration and teaching tool. While it is fully functional otherwise, it has thus been compiled imposing more stringent limits on the size of the models which can be fitted than for the Linux versions.
• Note also, that by default Cygwin limits the amount of memory available to a program to 384 MB. This can be changed if your machine has more memory available; see the Cygwin User's Guide for details.

Further links

• The Cygwin User's Guide
• Documentation for the g95 compiler, including a manual and a list of run time error messages issued by the compiler.
• Looking for a Linux distribution to install ? Check out Kubuntu.

© 2007 K. Meyer · Design by Andreas Viklund