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Adds instructions for singularity installation to docs
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samhorsfield96 committed Apr 27, 2023
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Expand Up @@ -13,7 +13,7 @@ We plan to get a MacOS version up and running in the future.
Installing with Docker (recommended)
-----------------------------------

First, install (`Docker <https://docs.docker.com/get-docker/>`_) for your OS. If running with WSL2, you should still download Docker Desktop for Windows.
First, install `Docker <https://docs.docker.com/get-docker/>`_ for your OS. If running with WSL2, you should still download Docker Desktop for Windows.

To use the latest image, run::

Expand All @@ -35,6 +35,20 @@ To run ggCaller from a local Docker build, run::

cd test && docker run --rm -it -v $(pwd):/workdir ggc_env:latest ggcaller --refs pneumo_CL_group2.txt

Installing with singularity
-----------------------------------

If you encounter permissions issues using Docker, you can download the singularity image from `Zenodo <https://zenodo.org/record/7870950>`_

Once downloaded, set up the singularity container using::

singularity shell --writable <singulatiry image>.sif

Once loaded, add the conda bin directory to your path variable and run ggCaller as normal::

PATH=$PATH:/opt/conda/bin
ggcaller --refs input.txt --out output_path

Installing with conda
-----------------------------------

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