The biomanycores bioperl library.
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http://www.biomanycores.org
The package provides Perl modules to interface bioperl objects and biomanycores tools.
Currently the interface is very light, but it allows you to launch the programs and run them on data contained in BioPerl objects.

How to install ?
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You need bioperl (at least 1.52) to use the modules. 
You will also need the module File::Temp and Config::Simple for SWcuda, pknotsRG, cudaPWM. For gpuHmmer, you need the BioPerl-Run package (at least 1.52) (gpuHmmer is an extension of the  Bio::Tools::Run::Hmmer wrapper).
You will have to install biomanycores applications (see www.biomanycores.org), and then to edit the configuration file biomanycores.ini in order to set paths and program names accordingly to your installation.
The package Biomanycores contains one separate perl module for each application. 

Demo programs
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SWcuda: Smith-Waterman alignment
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Perl module:  Biomanycores::PadovaSW.pm
This module provides an interface to run the alignment programm on Bioperl sequence objects.
You will have to set the name of the directory containing the executable program (swcuda) and the config file.
You can choose to run swcuda on cpu only or on gpu (default).
See bpcuda.pl for an example on how to use this module.

pknotsRG: pseudonots of an RNA sequence (EXPERIMENTAL)
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Perl module: Biomanycores::BielefeldPknots.pm
This module provides an interface to run the pknotsRG programm on bioperl sequence objects.
You will have to set the name of the directory containing the executable program (pknotsRG).
You can choose to run swcuda on cpu only or on gpu (default).
See bppknots.pl for an example on how to use this module.

cudaPWM: scan a position weight matrix against a DNA sequence
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Perl module: Biomanycores::LillePWM.pm
This module provides an interface to run the CUDApwm programm on bioperl objects.
You will have to set the name of the directory containing the executable program (pknotsRG).
You can choose to run swcuda on cpu only or on gpu (default).
See bppwm.pl for an example on how to use this module.

gpuHmmer: cuda version of hmmsearch tool
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Perl module: Biomanycores::gpuHmmer.pm (for bioperl-run < 1.6, you also need HmmerWrapper.pm)
This module extends Bio::Tools::Run::Hmmer (for bioperl-run 1.6) It provides a method to run cuda_hmmsearch, instead of hmmsearch.
Bio::Tools::Run::Hmmer is a wrapper for local execution of the hmmer suite (hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch). cuda_hmmer program must be in your path, or you must set the environment
variable HMMERDIR to point to its location.
See gpuhmmer.pl for an example on how to use this module.