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toniher authored Jul 24, 2021
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Expand Up @@ -9,22 +9,23 @@ The pipeline uses a set of well characterised software to assign functional info
The software used in this pipeline is mostly free software for academic users. For some software, such as signalP, a suitable license agreement should be obtained. More details about how to use this software in the *Associated containers* section.

## Installation
The pipeline is built on Nextflow as a woking engine, so it need to be installed first:

If you want to use the ```latest``` version you can clone the last commit of the repository:

```
export NXF_VER=20.10.0; curl -s https://get.nextflow.io | bash
git clone --–depth 1 https://github.com/guigolab/FA-nf
```
The detailed procedure is described in the [Nextflow documentation](https://www.nextflow.io/docs/latest/getstarted.html)

You can place the Nextflow binary somewhere in your ```PATH``` or in the same location as where you are going to run the pipeline.
Alternately, and actually recommended, you can clone the whole repository and choose the tag you want with ```git checkout``` command, or download a specific release from: https://github.com/guigolab/FA-nf/releases

If you want to use the ```latest``` version you can clone the last commit of the repository:
Since the pipeline is built on Nextflow as a woking engine, it needs to be installed as well:

```
git clone --–depth 1 https://github.com/guigolab/FA-nf
export NXF_VER=20.10.0; curl -s https://get.nextflow.io | bash
```
The detailed procedure is described in the [Nextflow documentation](https://www.nextflow.io/docs/latest/getstarted.html)

Alternately you can clone the whole repository and choose the tag you want with ```git checkout``` command, or download a specific release from: https://github.com/guigolab/FA-nf/releases
You can place the Nextflow binary somewhere in your ```PATH``` or in the same location where the pipeline is going to be run.

### Associated containers

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