GenDBWiki/AdministratorDocumentation/DependenciesAndRequirements: Difference between revisions
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* Perl >= 5.8.3 (please see the Perl bundle file on the GenDB ftp download site) | * Perl >= 5.8.3 (please see the Perl bundle file on the GenDB ftp download site) | ||
You will need to install a number of Perl modules, e.g. XML/DOM.pm, Config::[[IniFiles]] | |||
* BioPerl >= 1.4 | * BioPerl >= 1.4 | ||
* Apache 2 (mod_perl_2, ...) | * Apache 2 (mod_perl_2, ...) | ||
* Sun Grid Engine >= 6.0 | * Sun Grid Engine >= 6.0 | ||
* either a local sequence retrieval system or access to a remote system (e.g. SRS) | * either a local sequence retrieval system or access to a remote system (e.g. SRS) | ||
* MySQL >= | * MySQL >= 4.x | ||
* BLAST, InterPRO, HMMer, GLIMMER, Critica, ... (please see the list from the GenDB wiki section for details, the more tools, the better your annotations) | * BLAST, InterPRO, HMMer, GLIMMER, Critica, ... (please see the list from the GenDB wiki section for details, the more tools, the better your annotations) | ||
* Databases: EMBL, TrEMBL, UniProt, InterPro, Swissprot, KEGG, COG, GO, ... | * Databases: EMBL, TrEMBL, UniProt, InterPro, Swissprot, KEGG, COG, GO, ... | ||
Latest revision as of 07:17, 26 October 2011
GenDB Dependencies and Requirements
We run GenDB on a cluster of >= 350 CPUs. A genome of 5MB will take about a day to be annotated completely automatically, depending on the number of tools and databases, a serious amount of CPUs is required. To install GenDB you need at least the following software installed on your Linux/UNIX system:
- Perl >= 5.8.3 (please see the Perl bundle file on the GenDB ftp download site)
You will need to install a number of Perl modules, e.g. XML/DOM.pm, Config::IniFiles
- BioPerl >= 1.4
- Apache 2 (mod_perl_2, ...)
- Sun Grid Engine >= 6.0
- either a local sequence retrieval system or access to a remote system (e.g. SRS)
- MySQL >= 4.x
- BLAST, InterPRO, HMMer, GLIMMER, Critica, ... (please see the list from the GenDB wiki section for details, the more tools, the better your annotations)
- Databases: EMBL, TrEMBL, UniProt, InterPro, Swissprot, KEGG, COG, GO, ...
- for the GUI interface:
- Gtk 1.2.10 (more or less complete, 2.x will not work)
- Gnome 1.4 (including the Gnome Canvas, 2.x will not work )
- perl-gtk and bindings to Gnome (see http://gtk.org)