Installing the PipTools Programs   (all-Perl version)

TABLE OF CONTENTS

• General Outline
• Sample Walk-Throughs For Various Systems

General Outline

1. Make sure you have the necessary software available on your system:

   • Perl.   To run the Perl programs in the PipTools package, you will need a Perl interpreter (see the Perl Home Page for more information).

   • The Boulder::Genbank module.   This is a Perl module that is used by  genbank2exons  and  genbank2repeats  to read GenBank files. You can download it from the Stein Laboratory.

2. Download  piptools-perl.zip  and unpack it into a separate directory or folder. We provide this file in a DOS-style PKZIP-compatible format, because most platforms have readily available tools for handling this (e.g.,  unzip  on Unix.) Make sure your unzipper program recreates the subdirectory structure (e.g., by using  pkunzip -d ).

3. Arrange for the Perl interpreter to be executed when you run the tools. On Unix-like systems that support the  "#!"  syntax, this means making sure each program file is executable, and adjusting the path to  perl  in the first line. On other systems, you may need to set up wrapper scripts, or remember to type  perl -S  at the beginning of each command.

4. Make sure the installed program files are in your path, so your operating system can find them when you try to run them from another directory or folder.

Sample Walk-Throughs For Various Systems

• Win98 PC