Bioperl
Bioperl is a set of scripts in Perl language to aid researchers in Computational Biology and Bioinformatics.
Installation
Install bioperlAUR from the AUR.
Configuration
If you installed from the AUR 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. 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
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
Extras
The package Bioperl-run, which provides wrapper modules around many common bioinformatics applications and tools, is not installed by default.
sudo 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:
sudo cpan install Module::Name q