InstallationSystemWiki/Components

"Software" Documentation - Installationsystem - Components

This page describes the available components, their dependencies and configuration settings.

Table of components:

• common
• wrapper
• projectmanagement
• GOPArc
• GenDB - core component
• SEED
• GenDB - web interface

Notes:

• if a required perl module is not available by CPAN, a link to the download location is given

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common

Description

common provides a number of Perl modules that are used in almost all other components

Dependencies

other components: none Perl modules:

• Config::IniFiles
• Digest::MD5
• LWP::UserAgent
• HTTP::Request
• GD
• URI
• Schedule::DRMAAc

Configuration settings

SGE_ROOT	the root directory of SGE 6.0 or higher
SGE_CELL	the SGE cell to be used for submitting jobs. Defaults to 'default'

wrapper

Description

Perl wrapper for bioinformatics applications. These wrapper simplify the use of these application.

Dependencies

components:

• common

perl modules:

• Bio::SearchIO (part of the BioPerl package)

Configuration settings

CRITICA_LIB_DIR	the directory containing the binary files provides by the critica package
BLASTALL	the pathname of the blastall binary (NCBI blast version 2)
GLOBAL_TMP_DIR	a network-wide read- and writable directory used for temporary files generated by the critica wrapper
NT_DATABASE	a nucleotide database like nt (NCBI) or EMBL (EBI) or a stripped down subset. Used by the critica wrapper
GLIMMER_LIB_DIR	the direcotry containing the binary files of the glimmer package
INTERPRO_DIR	the directory containing the InterPROscan installation
GNU_MAKE	a gnu compatible version of the make utility

Notes:

• provides the wrapper scripts critica, glimmer and interpro_wrapper that may also be used standalone.
• the blast stage of Critica may be distributed by DRMAA. See critica usage message.
• the glimmer binaries need to be available for different genetic codes. Contact us for information how to build these different versions

gendb_web

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Author: Burkhard Linke