Installation

bio2zarr can either be installed from bioconda or PyPI.

By default the bio2zarr PyPI package does not come with dependencies needed to convert VCF or tskit files, so optional dependencies need to be specified:

python3 -m pip install bio2zarr #Base package with only plink support
python3 -m pip install bio2zarr[vcf] #Install with VCF support
python3 -m pip install bio2zarr[tskit] #Install with tskit support
python3 -m pip install bio2zarr[all] #Install with all optional dependencies

For bioconda users, a package with all optional dependencies already included is available in the bioconda channel:

conda install -c bioconda bio2zarr

This will install the programs vcf2zarr, vcf_partition, tskit2zarr and plink2zarr into your local Python path. You may need to update your $PATH to call the executables directly.

Alternatively, calling for example:

python3 -m bio2zarr vcf2zarr <args>

is equivalent to

vcf2zarr <args>

and will always work.

Warning

Windows support is preliminary, partial and needs to be fully documented. We recommend trying the bioconda packages in the first instance, and if this doesn’t work try using Windows Subsystem for Linux (WSL). Please comment on this issue if you would like to see improved Windows support for bio2zarr, or would like to help out with this.

Shell completion

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

eval "$(_VCF2ZARR_COMPLETE=bash_source vcf2zarr)"
eval "$(_TSKIT2ZARR_COMPLETE=bash_source tskit2zarr)"
eval "$(_PLINK2ZARR_COMPLETE=bash_source plink2zarr)"

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

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