BioPerl Dependencies

From BioPerl

The following packages are used by BioPerl. Not all are required for BioPerl to operate properly, however some functionality will be missing without them. You can easily choose to install all of these during the normal installation process. Note that the PPM version of the BioPerl packages always tries to install all dependencies.

Note:

Some modules require other applications or libraries to be installed.

• DBD::mysql - MySQL
• DB_File - Berkeley Database
• XML::Parser - expat
• GD - GD

NB: This list of packages is not authoritative. See the 'requires', 'build_requires' and 'recommends' sections of Build.PL instead.

Module	Where it is Used	Bio* Modules Affected
Ace [1]	Access to AceDB databases	Bio::DB::Ace
Bio::ASN1::EntrezGene	Parses ASN1 format	Bio::SeqIO::entrezgene, Bio::DB::EntrezGene
Class::AutoClass [2]	Used to create objects	Bio::Graph::SimpleGraph*
Clone	Used to clone objects	Bio::Graph::ProteinGraph
Convert::Binary::C	Parsing of DNA strider documents	Bio::SeqIO::strider
Data::Stag::ITextWriter	Structured Tags datastructures	Bio::SeqIO::chadoitext [3]
Data::Stag::SxprWriter	Structured Tags datastructures	Bio::SeqIO::chadosxpr [3]
Data::Stag::XMLWriter	Structured Tags datastructures	Bio::SeqIO::chadoxml
DB_File [4]	Perl access to Berkeley DB	Bio::DB::Flat, Bio::DB::Fasta, Bio::SeqFeature::Collection, Bio::Index::*
DBD::mysql [5]	MySQL API for loading and querying of MySQL-based GFF feature and BioSQL databases	Bio::DB::GFF, bioperl-db ,bioperl-pipeline
File::Temp	Temporary File creation	Bio::DB::FileCache, Bio::DB::XEMBL
GD [6] [7]	GD graphical drawing library	Bio::Graphics
Graph::Directed	Generic graph data and algorithms	Bio::Ontology::SimpleOntologyEngine
HTML::Entities	Parse BLAST results in XML	Bio::SearchIO::blastxml
HTML::Parser	HTML parsing of GDB page	Bio::DB::GDB
HTTP::Request::Common	GenBank,GenPept sequence retrieval, remote http BLAST jobs	Bio::DB::* Bio::Tools::Run::RemoteBlast
IO::String	handle to read or write to a string	Bio::SeqIO, Bio::Variation::*, Bio::DB::*, Bio::Index::Blast, Bio::Tools::*, Bio::Biblio::IO, Bio::Structure::IO
LWP::UserAgent	GenBank,GenPept sequence retrieval, remote http BLAST jobs	Bio::DB::*, Bio::Tools::Run::RemoteBlast
SOAP::Lite	SOAP protocol, XEMBL Services	Bio::Biblio::*, Bio::DB::XEMBLService
Spreadsheet::ParseExcel	Read Microsoft Excel files	Bio::SeqIO::excel
Storable	Persistent object storage & retrieval	Bio::DB::FileCache
Text::Shellwords	Text parser	Bio::Graphics::FeatureFile
Text::Wrap	Very optional	Bio::SearchIO::Writer::TextResultWriter
XML::DOM	XML parser	Bio::SeqIO::bsml, Bio::SeqIO::interpro
XML::Parser [8]	Parsing of XML documents	Bio::Biblio::IO::medlinexml
XML::Parser::PerlSAX	Parsing of XML documents	Bio::SeqIO::game, Bio::Variation::*, Bio::Biblio::IO::medlinexml
XML::SAX	New style SAX parser	Bio::SeqIO::bsml_sax, Bio::SeqIO::tigrxml, Bio::SearchIO::blastxml
XML::SAX::Base	New style SAX parser	Bio::SeqIO::tigrxml
XML::SAX::Writer
XML::Simple [8]	Simple SAX parser	Bio::DB::EUtilities
XML::Twig	Parsing of XML documents	Bio::Variation::IO::xml, Bio::DB::Biblio::eutils, Bio::Graph::IO::psi_xml
XML::Writer	Parsing + writing of XML documents	Bio::SeqIO::game, Bio::Variation::*

Notes

1. Available at http://stein.cshl.org [ace1]
2. Bio::Graph::SimpleGraph requires Class::AutoClass v. 1.01; earlier versions give very different results.

   [autoclass]

3. These modules may be present in older distributions but are considered redundant; use Bio::SeqIO::chadoxml instead.

   [deprecated]

4. Requires Berkeley DB, from Linux RPM or from http://www.sleepycat.com

   [berkeley]

5. Requires MySQL, from http://www.mysql.org

   [mysql]

6. Requires GD library (libgd) from http://www.boutell.com/gd

   [gd1]

7. Installing the GD library - libgd - is somewhat non-trivial since there are a number of dependencies to consider. Matías Giovannini has posted an excellent walkthrough for Mac OS X 10.4.

   [gd2]

8. Requires expat, at http://sourceforge.net/projects/expat/

   [expat1]