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MorphAdorner Northwestern
Introduction To Utilities

MorphAdorner provides a number of utility programs. The utility program names have fairly long Java classpaths, and the utility name is in mixed case. To simplify their use, all of the utilities have associated Windows batch files and Unix/Linux script files whose names are the utility name in lowercase.

In the following program descriptions, the command lines for the utilities may be split across multiple lines by your web browser or document reader. They should actually all appear on a single line. If you need to split the command lines you should terminate each line before the last with the command line continuation character for your operating system's command line shell. For Windows this is the caret "^". For Unix/Linux this is usually the back slash "\".

Don't forget to mark the Unix script files as executable before using them. On most Unix/Linux systems you can use the chmod command to do this, e.g.:

chmod 755 adornncfa

The MorphAdorner release contains a script makescriptsexecutable which applies chmod to each of the scripts in the release. On most Unix-like systems you can execute makescriptsexecutable by moving to the MorphAdorner installation directory and entering

chmod 755 makescriptsexecutable


/bin/sh <makescriptsexecutable

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