BioPerl Dependencies

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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.

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
Convert::Binary::C Parsing of DNA strider documents Bio::SeqIO::strider
Data::Stag::XMLWriter Structured Tags datastructures Bio::SeqIO::chadoxml
Data::Stag Structured Tags datastructures Bio::SeqIO::chaos
DB_File [2] Perl access to Berkeley DB Bio::DB::Flat, Bio::DB::Fasta, Bio::SeqFeature::Collection, Bio::Index::*
DBD::mysql [3] MySQL API for loading and querying of MySQL-based GFF feature and BioSQL databases Bio::DB::GFF, bioperl-db
File::Temp Temporary File creation Bio::DB::FileCache, Bio::DB::XEMBL
GD [4] [5] GD graphical drawing library Bio::Graphics
Graph::Directed Generic graph data and algorithms Bio::Ontology::SimpleGOEngine, Bio::PhyloNetwork
Graph Generic graph data and algorithms bioperl-network
HTML::Entities Parse BLAST results in XML Bio::SearchIO::blastxml
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
List::MoreUtils CAUSES TEST FAILURES (RATHER THAN DEPENDENCY FAILURE)
LWP::UserAgent GenBank,GenPept sequence retrieval, remote http BLAST jobs Bio::DB::*, Bio::Tools::Run::RemoteBlast
SOAP::Lite SOAP protocol, XEMBL Services Bio::Biblio::*
Set::Scalar
Spreadsheet::ParseExcel Read Microsoft Excel files Bio::SeqIO::excel
Statistics::Frequency
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::DOM::XPath
XML::Parser [6] 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 New style SAX parser Bio::SeqIO::tigrxml
SVG
XML::Simple [6] Simple SAX parser Bio::DB::EUtilities
XML::LibXML
XML::Twig Parsing of XML documents Bio::Variation::IO::xml, Bio::DB::Biblio::eutils
XML::Writer Parsing + writing of XML documents Bio::SeqIO::game, Bio::Variation::*

Notes

  1. Available at http://stein.cshl.org [ace1]
  2. Requires Berkeley DB, from Linux RPM or from http://www.sleepycat.com [berkeley]
  3. Requires MySQL, from http://www.mysql.org [mysql]
  4. Requires GD library (libgd) from http://www.boutell.com/gd [gd1]
  5. 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]
  6. Requires expat, at http://sourceforge.net/projects/expat/ [expat1]
  7. These modules may be present in older distributions but are considered redundant; use Bio::SeqIO::chadoxml instead. [deprecated]
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