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 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. Your operating system also needs internet access and a recent version of Python (3.10+).

Prerequisites

The 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:

Download the latest version of Python from the official website:
- Python Downloads
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:

Create a virtual environment:
```
python3 -m venv workflomics-env
```
Activate the virtual environment:
```
source workflomics-env/bin/activate
```

Installing Workflomics Benchmarker

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

Install workflomics-benchmarker using pip:
```
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:

Download Docker Desktop from the official website:
- Docker Downloads
Install Docker Desktop by following the installation guide for your OS and verify the installation:
```
docker --version
```

Installing Singularity/Apptainer

Alternatively, use Singularity (now Apptainer) for containerization:

Follow the installation guide on the official Apptainer documentation:
- Apptainer Installation Guide

Verify the installation:

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