Bioperl
Description
BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. Includes binaries and Perl modules useful in user scripts.
License
Use
For list of installed modules see the page Perl - modules.
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of bioperl and load default version of bioperl as
module avail bioperl/ # list available modules module load bioperl # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail bioperl
and choose explicit version you want to use.
To use libraries in own scripts try this:
#!/usr/bin/perl use Bio::Perl; own script code
The module contains (among others) Aliscore.
Documentation
Documentation is available in manual pages or at the project wiki.