Bioperl

From ArchWiki

Jump to: navigation, search
Image:Tango-document-new.png This article is a stub.
This typically means the article is a placeholder for more content to come. Knowledgeable users are encouraged to help expand the article.

Bioperl is a set of scripts in Perl language to aid researchers in Computational Biology and Bioinformatics.

Contents

Installation

You can find Bioperl in the AUR Here. The installation process makes use of yaourt to install packages from the AUR.

Dependencies

First install the dependencies:

sudo pacman -S perl
sudo pacman -S perl-io-string
sudo pacman -S expat
yaourt -S perl-data-stag

Then, the bioperl package should be installed without trouble:

yaourt -S bioperl

Configuration

If you installed from yaourt to the /usr folder (default), the path to bioperl should be added to the @INC array of perl. This is easily done editing the PERL5LIB variable in your .bashrc file, like this:

nano ~/.bashrc

Then adding this line to the end of the file:

export PERL5LIB=$PERL5LIB:/usr/share/perl5/site_perl/5.10.0

Note: Please take a look to the folder /usr/share/perl5/site_perl/ to see if the version is the same, the folder 5.10.0 (or a new version) should contain a folder named BIO. After saving the file, for the $PERL5LIB variable to be updated, bash must be reloaded in terminal:

bash

It is adviced to install extra modules from CPAN, to avoid having dependencies errors.

  • Upgrade CPAN
sudo perl -MCPAN -e shell
install Bundle::CPAN
q
  • Install/upgrade Module::Build, and make it your preferred installer
sudo cpan
install Module::Build
o conf prefer_installer MB
o conf commit
q

Troubleshooting

If you run into trouble while compiling your perl scripts, with an error like "Can't locate (Name of the Module) in @INC", Install the missing Modules like this:

sudo cpan
install Module::Name
q

More Resources

http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix

Personal tools