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.

First of all, we need to create a "project" for storing the data, restricting access to certain users etc.		<-2>
`add_gendb_project`	creates a new GenDB project by setting up a new database and registering the project to the project management
Afterwards, we can to import a contig into GenDB either in FASTA or EMBL/GenBank format.		<-2>
`import_FASTA.pl`	Import a FASTA file containing one or more contig sequences.
`import_EMBL_GBK.pl`	Import an EMBL or GenBank file.
In the next steps we can compute the automatic annotation.		<-2>
`run_gendb_pipeline.pl`	A script that creates a set of default tools for the co-ordinated prediction of regions and functions within a given project. The user therefore either can specify a single contig of a project or import a new contig sequence into the project. In both cases a set of default tools (e.g. Critica, Glimmer, various BLAST tools,Reganor) will automatically be created, will be set up for this contig and finally will be run. If for a specific contig results from a former run of this script already exist, the user can have them updated. This script uses the `ToolCreator.pm` wizard module.
`tool_creator.pl`	This script creates a default set of tools. You can either restrict the set of tools to region tools and function tools respectively or you can create both types. Additionally you can create a Metanor tool. This script also uses the `ToolCreator.pm` wizard module.
`submit_job.pl`	The computation of some bioinformatics tools can be started by using the GenDB job submitter.
After finishing our genome annotation we can export the results and create some nice plots.		<-2>
`export_EMBL_GBK.pl`	Export an EMBL or GenBank file for a single contig stored within a GenDB project.
`wholegenome_plot.pl`	Visualizes an overview of a contig in a chessboard style. User defined color schemes may be used to highlight groups of genes.
`genome_plot.pl`	Visualizes an overview of a contig as a circular genome map.
Finally, we can clean up our project by deleting a contig.		<-2>
`delete_contig.pl`	Delete a contig from a GenDB project. /!\ Running this script might take some time for large contigs with many subregions and computed observations.

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TODO:

• add more essential scripts