Installation

python3 -m pip install bio2zarr

This will install the programs vcf2zarr and vcf_partition into your local Python path. You may need to update your $PATH to call the executables directly.

Alternatively, calling

python3 -m bio2zarr vcf2zarr <args>

is equivalent to

vcf2zarr <args>

and will always work.

Note

The python3 -m bio2zarr vcf2zarr form may be replaced with python3 -m bio2zarr.vcf2zarr in the near future. See GitHub issue 203.

Warning

Windows is not currently supported. Please comment on this issue if you would like to see Windows support for bio2zarr.

Shell completion

To enable shell completion for a particular session in Bash do:

eval "$(_VCF2ZARR_COMPLETE=bash_source vcf2zarr)"

If you add this to your .bashrc vcf2zarr shell completion should available in all new shell sessions.

See the Click documentation for instructions on how to enable completion in other shells.