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Operations on GeneBe Hub Databases

Your databases are stored locally on your computer, allowing you to annotate variants without sending data to the server. To manage these databases, GeneBeClient provides several commands, all prefixed with annotate. For example, to use the pull command, you would write:

annotate pull

You can access help for any command by using the --help flag. For example:

annotate pull --help

Available Commands

• pull – Downloads a database from GeneBe Hub. You can specify a database using owner/name or owner/name:version. If no version is specified, the latest active version is downloaded.
• push – Uploads your database to the server, allowing you to share it with others. You can only push databases within your namespace, meaning the owner must be either your login or one of your organizations.
• list – Lists databases stored in your local repository.
• remove – Deletes a database from your local repository.
• create-* – A set of commands for creating new databases, described in another section of this help documentation.
• copy – Copies a database to a new name. This can be used for renaming databases, such as copying them into your namespace.
• dump – Extracts database contents into a different format. By default, databases are stored in parquet format, but you can dump them into more human-readable formats like tsv.
• export – Saves a database as a single .tar file, allowing you to share it outside of GeneBe Hub.
• import – Imports a database that was previously exported using the export command.
• check – Validates the database.
• describe – Displays a short description of a database in your local repository.