Bioperl - ArchWiki

# Bioperl

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

## Installation

Install bioperlAUR[broken link: archived in aur-mirror] from the AUR.

## Configuration

If you installed from the AUR to the `/usr` path (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 at folder `/usr/share/perl5/site_perl/` to see if the version is the same, the folder 5.10.0 (or a newer version) should contain a folder named BIO. If nor 5.10.0 neither other version is found, look for the Bio folder in `vendor_perl` or any other perl5 folder where the Bio folder may have been installed, add the path where the Bio folder is to the bash file.

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

    # perl -MCPAN -e shell
    install Bundle::CPAN
    q

- Install/upgrade Module::Build, and make it your preferred installer

    # cpan
    install Module::Build
    o conf prefer_installer MB
    o conf commit
    q

## Extras

The package Bioperl-run, which provides wrapper modules around many common bioinformatics applications and tools, is not installed by default.

    # cpan
    d /bioperl/

Which would return something like this:

    Distribution    BIRNEY/bioperl-1.2.2.tar.gz
    Distribution    BIRNEY/bioperl-1.2.3.tar.gz
    Distribution    BIRNEY/bioperl-1.2.tar.gz
    Distribution    BIRNEY/bioperl-1.4.tar.gz
    Distribution    BIRNEY/bioperl-db-0.1.tar.gz
    Distribution    BIRNEY/bioperl-ext-1.4.tar.gz
    Distribution    BIRNEY/bioperl-gui-0.7.tar.gz
    Distribution    BIRNEY/bioperl-run-1.4.tar.gz
    Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
    Distribution    CJFIELDS/BioPerl-1.6.0.tar.gz
    Distribution    CJFIELDS/BioPerl-1.6.1.tar.gz
    Distribution    CJFIELDS/BioPerl-db-1.6.0.tar.gz
    Distribution    CJFIELDS/BioPerl-network-1.6.0.tar.gz
    Distribution    CJFIELDS/BioPerl-run-1.6.1.tar.gz
    Distribution    CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
    15 items found

Then simply do (check the version compatibility):

    install CJFIELDS/BioPerl-run-1.6.1.tar.gz
    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:

    # cpan
    install Module::Name
    q

## See also

- Installing Bioperl for Unix

Category:

- Mathematics and science

Hidden category:

- Pages with broken package links