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There are four hardcoded variables you may need to set. Look in
deob_interface.cgi for a section labeled 'SET HARDCODED VALUES HERE'.

=over

=item C<< $deob_detail_path >>

The URL of the F<deob_detail.cgi> program. Set to L<<
http://localhost/cgi-bin/deob_detail.cgi >> by default. F<deob_detail.cgi>
needs to be in your webserver's F<cgi-bin> directory or some location where
you are allowed to serve executable code to the web.

If you are setting up the Deobfuscator package on your own machine, the
default URL will probably work. Otherwise, you will need to change the URL,
replacing the C<< localhost portion >> with the hostname of your webserver,
and replacing C<< cgi-bin >> with the path to F<deob_detail.cgi> (starting
at your webserver's root directory).

=item C<< $PERLMODULES >>

The textfile containing a list of the BioPerl modules. Set to
F<package_list.txt> by default. F<package_list.txt> is automatically generated
by the L<< deob_index.pl >> script and its name is a hardcoded value.

If your copy of F<package_list.txt> has a different name or is not in the
same directory as F<deob_detail.cgi>, set $PERLMODULES to the full path of
F<package_list.txt>'s location.

=item C<< $BerkeleyDB_packages >>

The Berkeley DB file storing documentation on BioPerl packages. Set to
F<packages.db> by default. F<packages.db> is automatically generated by the
L<< deob_index.pl >> script and its name is a hardcoded value.

If your copy of F<packages.db> has a different name or is not in the same
directory as F<deob_detail.cgi>, set C<< $BerkeleyDB_packages >> to the
full path of F<packages.db>'s location.

=item C<< $BerkeleyDB_methods >>

The Berkeley DB file storing documentation on BioPerl methods. Set to F<methods.db> by default. F<methods.db> is automatically generated by the
F<deob_index.pl> script and its name is a hardcoded value.

If your copy of F<methods.db> has a different name or is not in the same
directory as F<deob_detail.cgi>, set C<< $BerkeleyDB_methods >> to the
full path of  F<methods.db>'s location.

=back


=head1 DEPENDENCIES

L<version>, L<CGI>, L<Deobfuscator>


=head1 INCOMPATIBILITIES

None reported.


=head1 BUGS AND LIMITATIONS

=over

=item C<< Selecting a class name returns no methods >>

Clicking on C<< Bio::Tools::dpAlign >> or C<< Bio::Tools::AlignFactory >> in
the upper class selection pane produces an empty lower methods pane. There are
undoubtedly other modules that will display this behavior. Reported by Laura
Kavanaugh 2006-04-18.

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.

  bioperl-l@bioperl.org                       - General discussion
  http://bioperl.org/Support.html   - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues


=head1 SEE ALSO

L<Deobfuscator>, L<deob_detail.cgi>, L<deob_index.pl>


=head1 AUTHOR

Laura Kavanaugh


=head1 CONTRIBUTORS

=over

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

=item David Curiel

=back


=head1 ACKNOWLEDGMENTS

This software was developed originally at the Cold Spring Harbor Laboratory's
Advanced Bioinformatics Course between Oct 12-25, 2005. Many thanks to David
Curiel, who provided much-needed guidance and assistance on this project. Also, special thanks to Todd Wylie for his help with CGI.

=head1 LICENSE AND COPYRIGHT