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Table 1 Software dependencies

From: GMODWeb: a web framework for the generic model organism database

Package name Version GMOD tool Description
postgresql-server    The PostgreSQL database server
postgresql ≥7.3   Client libraries for PostgreSQL
perl-Apache-ParseFormData    A Perl library for accessing form data in mod_perl
perl-Class-Base    A Perl base class for other modules
perl-Class-DBI    A Perl tool for abstracting database access
perl-Class-DBI-ConceptSearch    A flexible Perl module for searching databases
perl-Class-DBI-Pager    A Perl tool for breaking database query results into pages
perl-Class-DBI-Pg    A PostgreSQL driver for Class::DBI
perl-Class-DBI-Plugin-Type    A Perl tool for determining data type information
perl-DBD-Pg    A PostgreSQL driver for Perl
perl-DBI    A generic database interface for Perl
perl-Log-Log4perl    Logging software for Perl applications
perl-SQL-Translator    A Perl tool for translating SQL schema into an object model
perl-Template-Toolkit    A template engine for Perl
perl-XML-LibXML    An XML parsing library for Perl
perl-Lucene    A Lucene search engine interface for Perl
perl-Apache2-SOAP    Automatic SOAP bindings for mod_perl
perl-Cache-Cache    A Perl tool used to cache web pages in GMOD-Web
httpd    The Apache webserver
mod_perl ≥2.0.1   A plugin for Apache that executes Perl code
perl    An interpreted language used throughout the Turnkey/GMODWeb project
gbrowse   Yes A genome feature browser web application from the GMOD project
textpresso   Yes A literature search web application from the GMOD project
AmiGO   Yes An ontology browser web application from the GMOD project
chado   Yes A sample Chado database from the GMOD project
chado-schema   Yes The Chado schema from the GMOD project
gmod-web ≥1.3 Yes A GMODWeb site generated with Turnkey for the Chado schema
turnkey ≥1.3   The website generation tool used to create GMODWeb
  1. The GMODWeb application has many software dependencies. This table shows the immediate GMODWeb and Turnkey dependencies on the Fedora Core 2 Linux distribution. All dependencies are available from the Biopackages software repository [39] or are provided by the underlying operating system