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hariszaf committed Jul 26, 2023
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8 changes: 0 additions & 8 deletions docs/faq.rst
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Expand Up @@ -29,16 +29,8 @@ metaGOflow supports both Docker (default) and Singularity container technologies
By default, metaGOflow will use Docker; therefore, in this case Docker is a dependency for the workflow to run.
However, in most HPC systems Singularity is preferred.

To enable Singularity, you need to add the `-s` argument when calling metaGOflow.
In case Singularity runs fail with an error message mentioning that a `.sif` file is missing,
you need to force-pull the images to be used from metaGOflow.
To make things easier, we have built the [get_singularity_images.sh](https://github.com/emo-bon/pipeline-v5/blob/develop/Installation/get_singularity_images.sh) to do so.

.. code-bloc:: bash
cd Installation
bash get_singularity_images.sh

Now, you are ready to run metaGOflow with Singularity!

.. hint:: In case you are using Docker, it is strongly recommended to avoid installing it through `snap`.

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9 changes: 9 additions & 0 deletions docs/installation.rst
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Expand Up @@ -56,4 +56,13 @@ In case ``conda`` is not already installed on your computing system, you may fol
the instructions to get it `here <https://conda.io/projects/conda/en/latest/user-guide/install/index.html>`_.


In case Singularity runs fail with an error message mentioning that a `.sif` file is missing,
you need to force-pull the images to be used from metaGOflow.
To do so, you may run the ``get_singularity_images.sh`` [`url <https://github.com/emo-bon/pipeline-v5/blob/develop/Installation/get_singularity_images.sh>`_] script
that you shall find under the ``Installation`` folder.

.. code-bloc:: bash
cd Installation
bash get_singularity_images.sh


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