Usage

After installation you can use the DivBrowse CLI to start a local instance of DivBrowse on your computer. You only have to provide a .vcf/.vcf.gz file and a .gff/.gff3 file in a subdirectory. Within the subdirectory you can start a DivBrowse instance via the following command:

$ divbrowse start --infer-config

An attempt is made to infer the configuration from the data provided. A Zarr archive of the provided VCF file is automatically created and saved in the same directory as the VCF file with .zarr appended to the original filename of the provided VCF file.

If you want to improve and customize the configuration, you can take the example config YAML file divbrowse.config.yml.example (click to open) file from the GitHub repository, rename it to divbrowse.config.yml and edit it to fit your requirements.

If you provide a manually written divbrowse.config.yml, you can start a DivBrowse instance using this customized configuration by executing the following CLI command in the directory consisting your custom config YAML file:

$ divbrowse start

Manual conversion of VCF file to Zarr format

The CLI allows to convert VCF files to Zarr archives independently:

$ divbrowse vcf2zarr –path-vcf /path/to/my_variants.vcf.gz –path-zarr /path/to/my_variants.zarr

The created Zarr archive can then be used in the configuration settings file divbrowse.config.yml as data source for the variant data:

datadir: /path/to/

variants:
  zarr_dir: my_variants.zarr

DivBrowse CLI reference

divbrowse

This is the DivBrowse CLI

divbrowse [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

start

divbrowse start [OPTIONS]

Options

--host <host>

IP address to bind the DivBrowse server to

Default

0.0.0.0

--port <port>

Port number to bind the DivBrowse server to

Default

8080

--infer-config

If set: infer a basic configuration from the provided VCF and GFF/GFF3 files and do not use an existing divbrowse.config.yml

--save-config <save_config>

Save the inferred configuration as a YAML file. Please provide a relative or absolute path.