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chore(docs): update install instructions
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mbhall88 committed Sep 24, 2024
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Expand Up @@ -45,7 +45,10 @@ $ conda install -c bioconda nohuman

### Precompiled binary

Note: you will need to [install kraken2][kraken] yourself using this install method.
![GitHub Downloads (all assets, all releases)](https://img.shields.io/github/downloads/mbhall88/nohuman/total)

> [!IMPORTANT]
> You will need to [install kraken2][kraken] yourself using this install method.
```shell
curl -sSL nohuman.mbh.sh | sh
Expand Down Expand Up @@ -89,7 +92,8 @@ Options

![Crates.io](https://img.shields.io/crates/d/nohuman)

Note: you will need to [install kraken2][kraken] yourself using this install method.
> [!IMPORTANT]
> You will need to [install kraken2][kraken] yourself using this install method.
```shell
$ cargo install nohuman
Expand All @@ -99,20 +103,20 @@ $ cargo install nohuman

Docker images are hosted on the GitHub Container registry.

#### `singularity`
#### `apptainer`

Prerequisite: [`singularity`][singularity]
Prerequisite: [`apptainer`][apptainer] (previously `singularity`)

```shell
$ URI="docker://ghcr.io/mbhall88/nohuman:latest"
$ singularity exec "$URI" nohuman --help
$ apptainer exec "$URI" nohuman --help
```

The above will use the latest version. If you want to specify a version then use a
[tag][ghcr] like so.

```shell
$ VERSION="0.1.1"
$ VERSION="0.2.1"
$ URI="docker://ghcr.io/mbhall88/nohuman:${VERSION}"
```

Expand All @@ -129,7 +133,8 @@ You can find all the available tags [here][ghcr].

### Build from source

Note: you will need to [install kraken2][kraken] yourself using this install method.
> [!IMPORTANT]
> You will need to [install kraken2][kraken] yourself using this install method.
```shell
$ git clone https://github.com/mbhall88/nohuman.git
Expand Down Expand Up @@ -313,7 +318,7 @@ more details and for other alternate approaches.

[quay.io]: https://quay.io/repository/mbhall88/nohuman

[singularity]: https://sylabs.io/guides/3.5/user-guide/quick_start.html#quick-installation-steps
[apptainer]: https://github.com/apptainer/apptainer

[docker]: https://docs.docker.com/v17.12/install/

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