InstallationSystemWiki/Components: Difference between revisions
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<span id="common"></span> | |||
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<span id="wrapper"></span> | |||
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* 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 | ||
<span id="projectmanagement"></span> | |||
== projectmanagement == | == projectmanagement == | ||
<span id="goparc"></span> | |||
== goparc == | == goparc == | ||
<span id="gendb_core"></span> | |||
== gendb == | == gendb == | ||
<span id="seed"></span> | |||
== SEED == | == SEED == | ||
<span id="gendb_web"></span> | |||
== gendb_web == | == gendb_web == | ||
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Author: [http://www.cebitec.uni-bielefeld.de/~blinke Burkhard Linke] | Author: [http://www.cebitec.uni-bielefeld.de/~blinke Burkhard Linke] | ||
Latest revision as of 07:13, 26 October 2011
"Software" Documentation - Installationsystem - Components
This page describes the available components, their dependencies and configuration settings.
Table of components:
Notes:
- if a required perl module is not available by CPAN, a link to the download location is given
common
Description
common provides a number of Perl modules that are used in almost all other components
Dependencies
other components: none Perl modules:
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
projectmanagement
goparc
gendb
SEED
gendb_web
Author: Burkhard Linke