Bio::BioStudio SEE ALSO Bio::GeneDesign DEPENDENCIES The Perl libraries not in the Perl core that BioStudio requires are Text::Diff, Time::Format, Exception::Class, Digest::MD5, URI::Escape, Readonly, and YAML::Tiny. All of these perl libraries can be installed by BioStudio at install time or beforehand with cpan. You need BioPerl-live, from github and not from cpan. git clone https://github.com/bioperl/bioperl-live.git cd bioperl-live/ sudo perl Build.PL sudo ./Build installdeps sudo ./Build test sudo ./Build install cd ../ git clone https://github.com/bioperl/bioperl-run.git cd bioperl-run/ sudo perl Build.PL sudo ./Build installdeps sudo ./Build install OPTIONAL PACKAGES If a graphical user interface is desired, the excellent GBrowse2 is available and easily installed from https://github.com/GMOD/GBrowse. For static graphic representations of chromosomes BioStudio requires the Cairo library and FreeType2 as well as the associated perl bindings Cairo and Font::FreeType. BLAST+ is required for sequence comparison and for PCRTag generation. Make sure you are using BLAST+ and not any older set of BLAST scripts. The package is available from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/. BioStudio's performance on large genomes is drastically improved by the indexing annotations in a relational database. MySQL 5.6 or Postgres 9.3 are supported. Make sure to install the perl libraries DBI and either DBD::mysql or DBD::Pg. INSTALLATION To install this module, run the following commands: perl Build.PL ./Build ./Build test ./Build install SUPPORT AND DOCUMENTATION After installing, you can find documentation for this module with the perldoc command. perldoc Bio::BioStudio You can also look for information at: RT, CPAN's request tracker (report bugs here) http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio::BioStudio AnnoCPAN, Annotated CPAN documentation http://annocpan.org/dist/Bio::BioStudio CPAN Ratings http://cpanratings.perl.org/d/Bio::BioStudio Search CPAN http://search.cpan.org/dist/Bio::BioStudio/ FUTURE WORK •Revamp the custom feature system so that they are described in individual files and stored as Bio::Root::Root objects (in concert with BioStudio) LICENSE AND COPYRIGHT Copyright (C) 2011 Sarah Richardson This program is distributed under the (Revised) BSD License: L Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Sarah Richardson's Organization nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.