BioPerl
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 is a one page summary of BioPerl that introduces several high level concepts and some points that are specifically important for GMOD. If you have a detailed question about BioPerl, see the BioPerl web site for more.
Contents
BioPerl Background
BioPerl Packages and bioperl-live
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 you which BioPerl packages are required for it to work.
BioPerl Releases
At any point in time there are generally 3 BioPerl releases:
| Release | Description | Use in GMOD? |
|---|---|---|
| Stable | Stable releases have gone through more testing than the other types of releases. They come out infrequently and as of January 2008, the most recent stable release was 1.4.0, released in December 2003. | No |
| Developer | Developer releases have gone through some testing, but less than stable releases. These come out more frequently than stable releases. As of January 2007, the latest developer release is 1.5.2, released in December 2006. | No |
| CVS HEAD / BioPerl-live | BioPerl-live 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. | Yes |
GMOD components rely on fixes and features that are not in either the stable or developer releases. You need to use BioPerl-live. See BioPerl's Using CVS and Getting BioPerl pages for how to get the latest copy of BioPerl-live.
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
You need to install external (i.e.,non-Perl) libraries before you install BioPerl. If these are not installed then attempts to install BioPerl will generate copious error messages.
If you are on Linux, then these will be available as packages 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. These are listed on BioPerl's installation pages.
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:
