| ... | ... | @@ -149,26 +149,23 @@ We use [snakemake](https://snakemake.readthedocs.io/en/stable/), a workflow mana |
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## Environment
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Softwares and dependencies can be run directly using environments such as containers or package management system.
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### Containers
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[](https://singularity-hub.org/collections/2878)
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We provide ready to run versions of container built with [Singularity containers](https://www.sylabs.io/). All required softwares to run the workflow have been installed within this container.
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We provide ready to run versions of [Singularity containers](https://www.sylabs.io/). All softwares you need to run the workflow have been installed into a container.
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User can either download the ready-to-use built container OR build this container instead to download it using the [Singularity.obitools](Singularity.obitools) recipe.
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To download this container :
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```
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singularity pull --name obitools.simg shub://Grelot/bioinfo_singularity_recipes:obitools
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```
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You will get a file named `obitools.simg`. Snakemake will need it to run softwares it contains.
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In both case, it gives an `obitools.simg` file. Absolute path to access to the container file fills the field `singularity:` into [config.yaml](config/)
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### Conda
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## Wildcards
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