diff --git a/docs/installation.md b/docs/installation.md index dc28f74..e2a8095 100644 --- a/docs/installation.md +++ b/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 $PATH to call the executables directly. -Alternatively, calling +Alternatively, calling for example: ```bash python3 -m bio2zarr vcf2zarr ``` @@ -21,16 +34,14 @@ vcf2zarr ``` and will always work. -:::{note} -The ``python3 -m bio2zarr vcf2zarr`` form may be replaced with -``python3 -m bio2zarr.vcf2zarr`` in the near future. -See GitHub issue [203](https://github.com/sgkit-dev/bio2zarr/issues/203). -::: - :::{warning} -Windows is not currently supported. Please comment on +Windows support is preliminary, partial and needs to be fully documented. +We recommend trying the bioconda packages in the first instance, and if +this doesn't work try using Windows Subsystem for Linux (WSL). +Please comment on [this issue](https://github.com/sgkit-dev/bio2zarr/issues/174) if you would -like to see Windows support for bio2zarr. +like to see improved Windows support for bio2zarr, or would like to +help out with this. ::: @@ -40,9 +51,11 @@ To enable shell completion for a particular session in Bash do: ```bash eval "$(_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)