HOWTO: Using the Amino Acid Preference Toolkit in a Windows Environment

• This toolkit has been developed within a Unix environment, so it currently has a bias towards that environment in that certain scripts are Unix shell scripts. The whole toolkit should run within a Windows environment, however, with only minor modifications. There are there major areas that need to be considered in moving to Windows:
  • All Java files - Java is a platform independent programming language so no changes need to be made to any of the Java files. They solely need to be compiled using the javac compiler on your system. For more information on Java and to obtain the latest release of the Java programming language, please see the Java homepage.

  • SVMLight toolkit - The SVMLight toolkit is written in the C programming language and is distributed in source code format. It can be compiled on any platform which has a C compiler, which includes Windows (using a tool such as Microsoft Visual C++) and Unix variants (Linux, Solaris, etc). Pre-compiled versions for four major platforms (Windows, Cygwin, Solaris, and Linux) are available from the SVMLight homepage.

  • Shell scripts (.sh files) - These files are Unix specific. They are used to control other processes, such as running two or more Java programs back to back and feeding the output of one into the other. These purpose of these scripts is to help automate parts of the toolkit processes. These files are easily convertable into Windows batch files (the equivalent of Unix shell scripts).