InstallationSystemWiki/Components - Revision history

Admin: 4 revisions

2011-10-26T06:13:21Z

4 revisions

← Older revision	Revision as of 08:13, 26 October 2011
(No difference)

imported>BurkhardLinke at 12:16, 1 December 2004

2004-12-01T12:16:47Z

← Older revision		Revision as of 14:16, 1 December 2004
Line 88:		Line 88:
	== projectmanagement ==		== projectmanagement ==

	~~[[Anchor(~~goparc]]		<span id="goparc"></span>
	== goparc ==		== goparc ==

imported>BurkhardLinke at 12:16, 1 December 2004

2004-12-01T12:16:06Z

← Older revision		Revision as of 14:16, 1 December 2004
Line 17:		Line 17:
	----		----

	~~[[Anchor(#~~common~~)]]~~		<span id="common"></span>
	== common ==		== common ==

Line 44:		Line 44:
	\|}		\|}

	~~[Anchor(~~wrapper)]		<span id="wrapper"></span>
	== wrapper ==		== wrapper ==

Line 85:		Line 85:
	* the glimmer binaries need to be available for different genetic codes. Contact [mailto:gendb@CeBiTec.Uni-Bielefeld.DE us] for information how to build these different versions		* the glimmer binaries need to be available for different genetic codes. Contact [mailto:gendb@CeBiTec.Uni-Bielefeld.DE us] for information how to build these different versions

	~~[[Anchor(#~~projectmanagement~~)]]~~		<span id="projectmanagement"></span>
	== projectmanagement ==		== projectmanagement ==

	[[Anchor(#goparc]]		[[Anchor(goparc]]
	== goparc ==		== goparc ==

	~~[[Anchor(#~~gendb_core~~)]]~~		<span id="gendb_core"></span>
	== gendb ==		== gendb ==

	~~[[Anchor(#~~seed~~)]]~~		<span id="seed"></span>
	== SEED ==		== SEED ==

	~~[[Anchor(#~~gendb_web~~)]]~~		<span id="gendb_web"></span>
	== gendb_web ==		== gendb_web ==

	----		----
	Author: [http://www.cebitec.uni-bielefeld.de/~blinke Burkhard Linke]		Author: [http://www.cebitec.uni-bielefeld.de/~blinke Burkhard Linke]

imported>BurkhardLinke at 12:13, 1 December 2004

2004-12-01T12:13:59Z

← Older revision	Revision as of 14:13, 1 December 2004
(No difference)

Unknown user at 00:00, 1 January 1970

1970-01-01T00:00:00Z

New page

__NOTOC__
= "Software" Documentation - Installationsystem - Components =

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

Table of components:
* [[#common|common]]
* [[#wrapper|wrapper]]
* [[#gpms|projectmanagement]]
* [[#goparc|GOPArc]]
* [[#gendb_core|GenDB - core component]]
* [[#seed|SEED]]
* [[#gendb_web|GenDB - web interface]]

Notes:
* if a required perl module is not available by [http://cpan.perl.org CPAN], a link to the download location is given
----

[[Anchor(#common)]]
== 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 =====
{| border="1" cellpadding="2" cellspacing="0"
| 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'
|}

[Anchor(wrapper)]
== 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 [http://www.bioperl.org BioPerl] package)

===== Configuration settings =====
{| border="1" cellpadding="2" cellspacing="0"
| 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 [mailto:gendb@CeBiTec.Uni-Bielefeld.DE us] for information how to build these different versions

[[Anchor(#projectmanagement)]]
== projectmanagement ==

[[Anchor(#goparc]]
== goparc ==

[[Anchor(#gendb_core)]]
== gendb ==

[[Anchor(#seed)]]
== SEED ==

[[Anchor(#gendb_web)]]
== gendb_web ==

----
Author: [http://www.cebitec.uni-bielefeld.de/~blinke Burkhard Linke]