Commit 75fb003a authored by Joanna Fourquet's avatar Joanna Fourquet
Browse files

Update usage.md

parent ef6d42fa
......@@ -93,10 +93,13 @@ Analyzing your metagenomic data with metagWGS allows you to use all **`nextflow
It allows you to choose the configuration profile among:
* `singularity` to analyze **your files** with metagWGS with **singularity containers**. You must have installed Singularity and downloaded the two Singularity containers associated to metagWGS (see [Installation page](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/installation.md)). Thus, your results will be reproducible. **NOTE:** there is no definition of the type of cluster (SGE, slurm, etc) you use in this profile.
* `conda` to analyze **your files** with metagWGS with **conda environments** already defined. You must have installed Miniconda (see [here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html)).
> **NOTE 1:** on [genologin cluster](http://bioinfo.genotoul.fr/) Miniconda is already installed: you can search Miniconda module with `search_module Miniconda`. Use of `conda` profile is easier than `singularity` profile but your results will be less reproducible.
**NOTE 2:** there is no definition of the type of cluster (SGE, slurm, etc) you use in this profile.
* `genotoul` to analyze **your files** with metagWGS **on genologin cluster** with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`.
* **NOTE 1:** Use of `conda` profile is easier than `singularity` profile but your results will be less reproducible.
* **NOTE 2:** there is no definition of the type of cluster (SGE, slurm, etc) you use in this profile. You can precise it into a `nextflow.config` file you can add into your working directory. For example if you are working on a slurm cluster, add this line to your `nextflow.config`:
```bash
process.executor = 'slurm'
```
* > **NOTE 3:** on [genologin cluster](http://bioinfo.genotoul.fr/) Miniconda is already installed: you can search Miniconda module with `search_module Miniconda` and load it with `module load chooosen_miniconda_module`.
* `genotoul` to analyze **your files** with metagWGS **on genologin cluster** with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`.
* `test_genotoul_workq` to analyze **small test data files** (used in [I. Basic Usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#i-basic-usage)) with metagWGS **on genologin cluster** on the **`workq`** queue with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`.
* `test_genotoul_testq` to analyze **small test data files** (used in [I. Basic Usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#i-basic-usage)) with metagWGS **on genologin cluster** on the **`testq`** queue with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`.
* `big_test_genotoul` to analyze **big test data files** (used in [Use case documentation page](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/use_case.md)) with metagWGS **on genologin cluster** (on the **`workq`** queue) with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`.
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