arch-wiki-md-repo

[Bioperl](http://bioperl.org/) is a set of scripts in the Perl programming language to aid researchers in [Computational Biology](https://en.wikipedia.org/wiki/Computational_biology "wikipedia:Computational biology") and [Bioinformatics](https://en.wikipedia.org/wiki/Bioinformatics "wikipedia:Bioinformatics"). ## Contents * [1 Installation](#Installation) * [2 Configuration](#Configuration) * [3 Extras](#Extras) * [4 Troubleshooting](#Troubleshooting) * [5 See also](#See_also) ## Installation Install [bioperl-live-git](https://aur.archlinux.org/packages/bioperl-live-git/) from the [AUR](/index.php/AUR "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 * [http://bioperl.org/INSTALL.html](http://bioperl.org/INSTALL.html)