Bioperl

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

Installation

Install bioperl-live-gitAUR 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