Bioperl
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: add PERL5LIB=$PERL5LIB:/usr/share/perl5/site_perl/5.10.0 as an environment variable.
/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.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