GenDBWiki/CoreDocumentation: Difference between revisions
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__NOTOC__ | __NOTOC__ | ||
= GenDB CORE Documentation | = GenDB CORE Documentation = | ||
This section describes the basic steps for automatically annotating a genome using the scripts provided with the GenDB CORE package. Each script has a detailed usage message that is displayed when a script is executed without any arguments. Please take a look at the documentation of each script for alternative options or advanced features. | This section describes the basic steps for automatically annotating a genome using the scripts provided with the GenDB CORE package. Each script has a detailed usage message that is displayed when a script is executed without any arguments. Please take a look at the documentation of each script for alternative options or advanced features. | ||
* | * ''import_EMBL_GBK.pl'' - | ||
* tool_creator.pl | * ''tool_creator.pl'' | ||
* submit_job.pl | * ''submit_job.pl'' | ||
* export_EMBL_GBK.pl | * ''export_EMBL_GBK.pl'' | ||
* delete_contig.pl | * ''delete_contig.pl'' | ||
* delete_contig_with_feedback.pl | * ''delete_contig_with_feedback.pl'' | ||
In addition to the scripts required for annotating a genome the GenDB CORE package includes a number of scripts for maintaining GenDB databases and projects listed below: | In addition to the scripts required for annotating a genome the GenDB CORE package includes a number of scripts for maintaining GenDB databases and projects listed below: | ||
* add_annotator.pl | * ''add_annotator.pl'' - This script can be used for adding a human annotator to a GenDB project database. Usually this is already done automatically by the GPMS. | ||
* cleanup_database.pl | * ''cleanup_database.pl'' - This script checks a number of GenDB objects for consistency. Objects with illegal references e.g. to already deleted objects are removed and deleted automatically. | ||
* optimize_tables.pl | * ''optimize_tables.pl'' - Use this script after larger database operations like computing several tools in order to optimize all tables automatically. | ||
* set_user_config.pl | * ''set_user_config.pl'' - A default user configuration can be transferred to a GenDB user account with this script. | ||
Revision as of 17:23, 11 October 2004
GenDB CORE Documentation
This section describes the basic steps for automatically annotating a genome using the scripts provided with the GenDB CORE package. Each script has a detailed usage message that is displayed when a script is executed without any arguments. Please take a look at the documentation of each script for alternative options or advanced features.
- import_EMBL_GBK.pl -
- tool_creator.pl
- submit_job.pl
- export_EMBL_GBK.pl
- delete_contig.pl
- delete_contig_with_feedback.pl
In addition to the scripts required for annotating a genome the GenDB CORE package includes a number of scripts for maintaining GenDB databases and projects listed below:
- add_annotator.pl - This script can be used for adding a human annotator to a GenDB project database. Usually this is already done automatically by the GPMS.
- cleanup_database.pl - This script checks a number of GenDB objects for consistency. Objects with illegal references e.g. to already deleted objects are removed and deleted automatically.
- optimize_tables.pl - Use this script after larger database operations like computing several tools in order to optimize all tables automatically.
- set_user_config.pl - A default user configuration can be transferred to a GenDB user account with this script.