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
Template:CPAN ace1 Access to AceDB databases Template:PM
Template:CPAN Parses ASN1 format Template:PM, Template:PM
Template:CPAN autoclass Used to create objects Template:PM*
Template:CPAN Used to clone objects Template:PM
Template:CPAN Parsing of DNA strider documents Template:PM
Template:CPAN Structured Tags datastructures Bio::SeqIO::chadoitext deprecated
Template:CPAN Structured Tags datastructures Bio::SeqIO::chadosxpr deprecated
Template:CPAN Structured Tags datastructures Template:PM
Template:CPAN berkeley Perl access to Berkeley DB Template:PM, Template:PM, Template:PM, Bio::Index::*
Template:CPAN mysql MySQL API for loading and querying of MySQL-based GFF feature and BioSQL databases Template:PM, bioperl-db ,bioperl-pipeline
Template:CPAN Temporary File creation Template:PM, Template:PM
Template:CPAN gd1 gd2 GD graphical drawing library Template:PM
Template:CPAN Generic graph data and algorithms Template:PM
Template:CPAN Parse BLAST results in XML Template:PM
Template:CPAN HTML parsing of GDB page Template:PM
Template:CPAN GenBank,GenPept sequence retrieval, remote http BLAST jobs Bio::DB::* Template:PM
Template:CPAN handle to read or write to a string Template:PM, Bio::Variation::*, Bio::DB::*, Template:PM, Bio::Tools::*, Template:PM, Template:PM
Template:CPAN GenBank,GenPept sequence retrieval, remote http BLAST jobs Bio::DB::*, Template:PM
Template:CPAN SOAP protocol, XEMBL Services Bio::Biblio::*, Template:PM
Template:CPAN Read Microsoft Excel files Template:PM
Template:CPAN Persistent object storage & retrieval Template:PM
Template:CPAN Text parser Template:PM
Template:CPAN Very optional Template:PM
Template:CPAN XML parser Template:PM, Template:PM
Template:CPAN expat1 Parsing of XML documents Template:PM
Template:CPAN Parsing of XML documents Template:PM, Bio::Variation::*, Template:PM
Template:CPAN New style SAX parser Template:PM, Template:PM, Template:PM
Template:CPAN New style SAX parser Template:PM
Template:CPAN
Template:CPAN expat1 Simple SAX parser Template:PM
Template:CPAN Parsing of XML documents Template:PM, Template:PM, Template:PM
Template:CPAN Parsing + writing of XML documents Template:PM, Bio::Variation::*

[edit] Notes

<biblio>

  1. ace1 Available at http://stein.cshl.org
  2. expat1 Requires expat, at http://sourceforge.net/projects/expat/
  3. mysql Requires MySQL, from http://www.mysql.org
  4. gd1 Requires GD library (libgd) from http://www.boutell.com/gd
  5. 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.
  6. berkeley Requires Berkeley DB, from Linux RPM or from http://www.sleepycat.com
  7. deprecated These modules may be present in older distributions but are considered redundant; use Template:PM instead.
  8. autoclass Template:PM requires Template:CPAN v. 1.01; earlier versions give very different results.

</biblio>

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