Installation guide
##################

This documentation provides instructions for setting up your local environment to benchmark workflows generated by the Workflomics web platform. The setup involves installing Python, setting up a virtual environment, installing the `Workflomics Benchmarker <https://github.com/Workflomics/workflomics-benchmarker>`_ and supporting containerization.

.. note:: If you are using Windows, you will have to install the Windows Subsystem for Linux 2 as documented in the Workflomics Benchmarker `documentation for Microsoft Windows users <https://github.com/Workflomics/workflomics-benchmarker/tree/main?tab=readme-ov-file#ms-windows-users>`_. Your operating system also needs internet access and a recent version of Python (3.10+).


Prerequisites
*************

The `Workflomics Benchmarker <https://github.com/Workflomics/workflomics-benchmarker>`_ requires the following environment:

- Linux, macOS, or WSL2 on Windows
- Python 3.10 or higher
- Docker or Singularity/Apptainer


Installing Python
*****************

Follow these steps to install Python:

1. Download the latest version of Python from the official website:

   - `Python Downloads <https://www.python.org/downloads/>`_

2. Follow the installation instructions for your operating system. Make sure to add Python to your system’s path.

Setting Up a Virtual Environment
********************************

After installing Python, proceed to set up a virtual environment for project dependencies:

1. Create a virtual environment:

   .. code-block:: bash

      python3 -m venv workflomics-env

2. Activate the virtual environment:

   .. code-block:: bash

      source workflomics-env/bin/activate

Installing Workflomics Benchmarker
**********************************

With the virtual environment activated, you can now install the Workflomics benchmarker:

1. Install `workflomics-benchmarker` using pip:

   .. code-block:: bash

      pip install workflomics-benchmarker


Supporting Containerization
***************************

Workflows generated by Workflomics are containerized. Depending on your preference, install Docker or Singularity/Apptainer.

Installing Docker
=================

Docker supports containerized environments:

1. Download Docker Desktop from the official website:

   - `Docker Downloads <https://www.docker.com/products/docker-desktop>`_

2. Install Docker Desktop by following the installation guide for your OS and verify the installation:

   .. code-block:: bash

      docker --version

Installing Singularity/Apptainer
================================

Alternatively, use Singularity (now Apptainer) for containerization:

1. Follow the installation guide on the official Apptainer documentation:

   - `Apptainer Installation Guide <https://apptainer.org/docs/user/main/quick_start.html#installation>`_

2. Verify the installation:

   .. code-block:: bash

      singularity version  # or `apptainer version` based on your installation