Quick start

This page provides instruction for installing RAFT and running a demonstration workflow in a local environment.

Note

Before you begin, make sure the following are installed on your system:

• Python 3.9+

• Nextflow

• Singularity or Apptainer

If any of these are missing, install them before running raft setup. See Running RAFT locally for more details.

Install RAFT

Users can install RAFT using

$ pip install --user reproducible-analyses-framework-and-tools

Initialize a RAFT workspace

RAFT can be initialized in the current directory using:

$ raft setup --default

Run a demonstration workflow

Run a demo workflow:

$ raft run-demo --workflow lens --version v1.9-dev

View example report

An example of a report can be viewed using:

$ raft generate-reports --demo

Note

A hosted example report using synthetic data is available here.

Run on your own data

Once you’re ready:

• See Choosing your environment to decide between local and cloud execution.

• See Choosing a workflow to find the right workflow for your data.

• See Preparing your samples for how to prepare your samples

• See either Running RAFT locally or Running RAFT on the cloud for a full overview of the run process.

• See Accessing and reviewing outputs for how to access outputs and review results