BioPerl

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BioPerl is a set of modules that support bioinformatics programming in Perl programs. BioPerl is used extensively by several GMOD components. You will need to install it before you can use those components.

This page gives you the background you need to understand BioPerl and then tells you how to get and install BioPerl.

If you are unfamiliar with BioPerl you are strongly encouraged to read the BioPerl Background section before moving on to the Installing BioPerl section.


BioPerl Background

BioPerl Web Site

The BioPerl project has an excellent web site at http://www.bioperl.org/. If you have a detailed question about BioPerl, the web site is the place to start.

However, the BioPerl web site is geared towards programmers who want to write programs that use BioPerl, and to developers who want to modify or extend BioPerl. Is is not particularly geared towards users who just need to install BioPerl to get another program (such as some of the GMOD Components) to work. It assumes a thorough knowledge of Perl.

This page links to BioPerl pages extensively, but also provides additional information that is assumed knowledge in the BioPerl web site.

BioPerl Packages

BioPerl is an enormous project. To make it more manageable it has been divided into several packages. The most popular package, and the one most frequently used by GMOD components is the Core package, also known as bioperl-live. Each GMOD component will tell which BioPerl packages are required for it to work.


BioPerl Releases

At any point in time there are generally 3 BioPerl releases to consider:

Release Description Where Use in GMOD?
Stable Stable releases have gone through more testing than the other types of releases. They come out infrequently and as of October 2007, the most recent stable release was 1.4.0, released in December 2003. BioPerl's Getting BioPerl This is too old for most GMOD components.
Developer Developer releases have gone through some testing, but less than stable releases. These come out more frequently than stable releases. As of October 2007, the latest developer release is 1.5.2, released in December 2006. BioPerl's Getting BioPerl This will work with some GMOD components, but you are probably better off using BioPerl-live.
CVS HEAD / BioPerl-live This is not a release per se, but is rather whatever happens to be in CVS on the day you got the files. This is the most up to date version of BioPerl you can get. It may also be entirely untested. BioPerl's BioPerl's Using CVS and Getting BioPerl Some GMOD components will require changes that have not yet been put in a release. You will need to use CVS HEAD for these components.

It is possible, but awkward, to have multiple releases installed at the same time. However, your life will be easier if you can pick one release and stick with it.

Installing BioPerl

Installing BioPerl is non-trivial. It has many dependencies both within and outside of Perl. Perl does a pretty good job of dealing with dependencies within Perl (meaning dependencies on other modules). It does not do so well with dependencies outside of Perl. You should address the external dependencies before attempting to install BioPerl.

Dependencies

Outside Perl

This section describes what external (non-Perl) libraries you will need to install before you install BioPerl. If these are not installed then attempts to install BioPerl will fail, often with hard to decipher error messages.

These libraries are required by BioPerl and must be installed on your system before installing BioPerl. If you are on Linux, then these will be available as package and should be installed using the appropriate package manager for your brand of Linux.

Library(ies) Description
perl-devel Perl development library.
perl-DB_File Berkeley DB support in Perl.
libgd, lbgd-devel Libraries for creating PNG, JPG, etc images.
expat, libexpat An XML parser.

Inside Perl

There are also a few Perl modules that you should install before installing BioPerl. What these are and how to install them is listed on BioPerl's installation pages. You will install these immediately before installing BioPerl.


Install

BioPerl has an Installing BioPerl page that includes pointers to specific platform installation pages. We follow the same pattern here. We have an installation page for each platform that includes a link to the BioPerl page and additional information to help clarify the BioPerl page.

Platforms: