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Add mention of PyPI to Wave docs
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Signed-off-by: Phil Ewels <[email protected]>
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ewels committed Nov 21, 2024
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2 changes: 2 additions & 0 deletions docs/conda.md
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Expand Up @@ -62,6 +62,7 @@ The usual Conda package syntax and naming conventions can be used. The version o

The name of the channel where a package is located can be specified prefixing the package with the channel name as shown here `bioconda::bwa=0.7.15`.

(conda-env-files)=
### Use Conda environment files

Conda environments can also be defined using one or more Conda environment files. This is a file that lists the required packages and channels structured using the YAML format. For example:
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The environment file name **must** have a `.yml` or `.yaml` extension or else it won't be properly recognised.
:::

(conda-pypi)=
### Python Packages from PyPI

Conda environment files can also be used to install Python packages from the [PyPI repository](https://pypi.org/)), through the `pip` package manager (which must also be explicitly listed as a required package):
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2 changes: 2 additions & 0 deletions docs/wave.md
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Expand Up @@ -90,6 +90,8 @@ conda.channels = 'conda-forge,bioconda'
```
:::

Packages from the [Python Package Index](https://pypi.org/) can also be used by using a Conda `environment.yml` file - see the documentation about {ref}`Conda and PyPI <conda-pypi>` for details.

(wave-singularity)=

### Build Singularity native images
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