GenDBWiki/CoreDocumentation/CoreScripts

GenDB Core Scripts

After installing and setting up the GenDB genome annotation system, the GenDB core scripts listed below can be used to annotate a genome without setting up a graphical user interface (neither the web frontend nor the Gtk GUI). After importing an EMBL or FASTA file you can create a set of tools for running the region and function prediction. After computing all bioinformatics tools, all genes can be annotated automatically and the results can be exported into different output format files. Furthermore, some scripts are provided for creating different plots and graphics. Last but not least your imported contigs can be deleted in order to cleanup the GenDB project database.

/!\ All scripts are used on your own risk, so have your backup prepared for the worst case! /!\

The scripts are part of the GenDB distribution and thus located in the `'gendb/share/exec/'` directory of your current GenDB environment. Execute all scripts from the `'gendb/bin/'` directory using the `'gendb_start'` wrapper script. Executing a script without any arguments gives a detailed usage message where all available options are explained. Please take a look at the documentation of each script for alternative options or advanced features.

• `import_EMBL_GBK.pl` - Import an EMBL or GenBank file.
• `tool_creator.pl` - Use this script to create a standard set of default tools for region and function prediction.
• `submit_job.pl` - The computation of some bioinformatics tools can be started by using the GenDB job submitter.
• `export_EMBL_GBK.pl` - Export an EMBL or GenBank file for a single contig stored within a GenDB project.
• `delete_contig.pl` - Delete a contig from a GenDB project.
  /!\ This might take some time for large contigs with many subregions and computed observations. /!\
  Usually you should use the script `'delete_contig_with_feedback.pl'` instead.
• `delete_contig_with_feedback.pl` - Delete a contig from a GenDB project and get some status information about the current progress.