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 ace1 |
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 berkeley |
Perl access to Berkeley DB |
Bio::DB::Flat, Bio::DB::Fasta, Bio::SeqFeature::Collection, Bio::Index::*
|
| DBD::mysql mysql |
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 gd1 gd2 |
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 expat1 |
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 expat1 |
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
<biblio>
- ace1 Available at http://stein.cshl.org
- expat1 Requires expat, at http://sourceforge.net/projects/expat/
- mysql Requires MySQL, from http://www.mysql.org
- gd1 Requires GD library (libgd) from http://www.boutell.com/gd
- gd2 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.
- berkeley Requires Berkeley DB, from Linux RPM or from http://www.sleepycat.com
- deprecated These modules may be present in older distributions but are considered redundant; use Bio::SeqIO::chadoxml instead.
</biblio>
