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May 23, 2025
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Update docs for deps and conda #408

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39 changes: 26 additions & 13 deletions docs/installation.md
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Original file line number Diff line number Diff line change
@@ -1,16 +1,29 @@
(sec-installation)=
# 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:
```bash
python3 -m pip install bio2zarr
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
```

This will install the programs ``vcf2zarr`` and ``vcf_partition``
into your local Python path. You may need to update your $PATH to call the
For bioconda users, a package with all optional dependencies already included
is available in the [bioconda channel](https://anaconda.org/bioconda/bio2zarr):
```bash
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
Alternatively, calling for example:
```bash
python3 -m bio2zarr vcf2zarr <args>
```
Expand All @@ -21,16 +34,14 @@ 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](https://github.com/sgkit-dev/bio2zarr/issues/203).
:::

:::{warning}
Windows is not currently supported. Please comment on
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](https://github.com/sgkit-dev/bio2zarr/issues/174) if you would
like to see Windows support for bio2zarr.
like to see improved Windows support for bio2zarr, or would like to
help out with this.
:::


Expand All @@ -40,9 +51,11 @@ To enable shell completion for a particular session in Bash do:

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

See the [Click documentation](https://click.palletsprojects.com/en/8.1.x/shell-completion/#enabling-completion)
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