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installation docs
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ncherric committed Aug 17, 2023
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.. _platform: https://iliad-readthedocs.readthedocs.io/en/latest/getting_started/platform_preparation.html
.. _token: https://docs.github.com/en/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls
.. _creation: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-fine-grained-personal-access-token

.. _login: https://cloud.google.com/?hl=en
.. _getting_started/installation:

============
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It still requires the installation of the native package manager for the Snakemake application itself and Singularity.
Many HPC users at an academic institution will already have Singularity on their clusters.

.. _conda-install:
.. image:: img/How-To-INTRO_Trim.mp4
:align: center
:width: 600

Google Cloud Platform server - Linux (Ubuntu)
====================================================================

First, you will have to use your google account or create one and login_.

Step 1: Install Snakemake and Snakedeploy
=============================================
*****************************************

Snakemake and Snakedeploy are best installed via the `Mamba package manager <https://github.com/mamba-org/mamba>`_ (a newer package manager for Conda replacement).
From our testing, Conda is perfectly fine as an alternative, and you can use them interchangeably below.
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**Estimated time: 15-20 minutes**

Step 2: Install Singularity
============================
***************************

Follow the `instructions guide <https://docs.sylabs.io/guides/3.6/user-guide/quick_start.html>`_ provided by Singularity to install the program under the
Operating System of your choosing.
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**Estimated time: 15-60 minutes**

Step 3: Clone the Iliad repository and workflows
================================================
************************************************

.. Given that Snakemake and Snakedeploy are installed and available (see Step 1), the workflow can be deployed as follows.
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Step 4: Configure Workflow
============================
**************************

To configure this workflow, modify ``Iliad/config/config.yaml`` according to your needs.
The file is clearly denoted into sections that you can change according to your needs.
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Step 5: Run workflow
============================
********************

Given that the workflow has been properly deployed and configured, it can be executed as follows.

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