Update docs for deps and conda

Author: benjeffery

docs/installation.md

@@ -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>
 ```
@@ -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.
 :::
 
 
@@ -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)