Table 1 |
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Software dependencies |
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|
Package name |
Version |
GMOD tool |
Description |
|
|
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|
postgresql-server |
The PostgreSQL database server |
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|
postgresql |
≥7.3 |
Client libraries for PostgreSQL |
|
|
perl-Apache-ParseFormData |
A Perl library for accessing form data in mod_perl |
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|
perl-Class-Base |
A Perl base class for other modules |
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|
perl-Class-DBI |
A Perl tool for abstracting database access |
||
|
perl-Class-DBI-ConceptSearch |
A flexible Perl module for searching databases |
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|
perl-Class-DBI-Pager |
A Perl tool for breaking database query results into pages |
||
|
perl-Class-DBI-Pg |
A PostgreSQL driver for Class::DBI |
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|
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 |
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|
perl-Cache-Cache |
A Perl tool used to cache web pages in GMOD-Web |
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|
httpd |
The Apache webserver |
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|
mod_perl |
≥2.0.1 |
A plugin for Apache that executes Perl code |
|
|
perl |
An interpreted language used throughout the Turnkey/GMODWeb project |
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|
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 |
|
|
|
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|
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 |
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O'Connor et al. Genome Biology 2008 9:R102 doi:10.1186/gb-2008-9-6-r102 |
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