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The kill_all() method only works with jobs submitted to a queueing system
right now. If you are itchin' to have this power over single jobs too, begging
via email would be appropriate.

=item C<< <num> weren't killed and still are in the queue >>

<num> jobs weren't successfully killed by kill_all() and are still on the
queue. You'll probably want to go kill them manually (or make another attempt
with kill_all() ).

=item C<< can't validate_blasts -- BPdeluxe 1.0 did not load. >>

BPdeluxe version 1.0 is needed to use the validate_blasts() method. The most
likely cause of this error is that BPdeluxe v1.0 isn't installed on your
system or it's in a directory that's not in @INC. BPdeluxe 1.0 is available
from Jarret Glasscock C<< <glasscock_cpan@mac.com> >>.

=item C<< validate_blasts only works on blast jobs >>

validate_blasts() will not work on any alignment program's output other than
one of the blast programs.

=back


=head1 CONFIGURATION AND ENVIRONMENT
  
AlignAid requires no configuration files or environment variables.


=head1 DEPENDENCIES

=over

=item Bio::SeqIO

part of BioPerl, available at bioperl.org

=item version

available from CPAN

=item PP

This is an optional dependency, needed if you want to submit jobs
to a compute cluster queueing system like LSF

=item BPdeluxe 1.0

This is an optional dependency, needed only if you want to use the
validate_blasts() method. Available from Jarret Glasscock
C<< <glasscock_cpan@mac.com> >>.

=back

=head1 INCOMPATIBILITIES

None reported.


=head1 BUGS AND LIMITATIONS

Spews Blast and cross_match STDERR all over the place.

No bugs have been reported.

Please report any bugs or feature requests to
C<dave-pause@davemessina.net>.


=head1 AUTHOR

Dave Messina  C<< <dave-pause@davemessina.net> >>


=head1 LICENCE AND COPYRIGHT

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

This module is free software; you can redistribute it and/or
modify it under the same terms as Perl itself. See L<perlartistic>.


=head1 DISCLAIMER OF WARRANTY

BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE
ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH
YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL
NECESSARY SERVICING, REPAIR, OR CORRECTION.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENCE, BE
LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL,
OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE
THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.

=head1 APPENDIX

The rest of the documentation details each of the functions.
Internal methods are preceded with a "_".

=cut

use version; $VERSION = qv('0.0.2');

use warnings;
use strict;
use Carp;

# determine if PP will be available
use vars qw($PP_loaded);