AlignAid version 0.0.2

AlignAid is a simple module which makes it easy to run sequence alignment
programs either locally or on a queue-based compute cluster. The user
specifies which alignment program to use, the queries and the database, and
what compute resources are available, and AlignAid takes care of the rest.

This capability is especially useful when you need to perform a large number
of alignments and have a compute cluster queue available; AlignAid will split
the task into multiple queue jobs, track their completion, and collate the
results.

The straightforward interface also comes in handy when you want to program to
adjust to the compute resources available to it. Using AlignAid, the program
could check for a queue and use it if available or run the alignments locally
if not.

For complete instructions, see the documentation for AlignAid by typing:

	perldoc AlignAid



INSTALLATION

To install this module, run the following commands:

    perl Makefile.PL
    make
    make test
    make install


Alternatively, to install with Module::Build, you can use the following commands:

    perl Build.PL
    ./Build
    ./Build test
    ./Build install



DEPENDENCIES

Bio::SeqIO   - part of BioPerl, available at bioperl.org
version      - available from CPAN
PP           - This is an optional dependency, needed if you want to submit
               jobs to a compute cluster queueing system like LSF.
BPdeluxe 1.0 - This is an optional dependency, needed only if you want to use
               the validate_blasts() method. Available from Jarret Glasscock
               (glasscock_cpan at mac dot com).




COPYRIGHT AND LICENCE

Copyright (C) 2006, Dave Messina <dave-pause@davemessina.net>.

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
