Bioperl
From ArchWiki
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