Quick Start

This page covers installing RAFT (the workflow manager that runs LENS) and running a built-in demonstration. By the end of this page you will have LENS running on real patient data.

Installing RAFT

RAFT is the Nextflow-based workflow manager that runs LENS. More information about RAFT is available at useraft.io.

Installing through Conda

Ensure Conda is installed prior to installing RAFT. Installation instructions are available on the Conda documentation page.

$ conda install -c bioconda -c conda-forge -c raft reproducible-analyses-framework-and-tools

Installing through pip

Installing RAFT through pip requires separately installing Apptainer and Git.

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

Note

pip will install raft to ~/.local/bin. Please ensure this directory is in your $PATH (export PATH=$PATH:~/.local/bin).

Setting up RAFT

RAFT requires a directory consisting of various folders including: /Projects, /References, and /Metadata. This directory will also contain the RAFT configuration file.

To set up RAFT, run:

$ raft.py setup

You will be prompted to provide paths for each required subdirectory (with sensible defaults).

A default installation (in which all subdirectories are created in the user’s current working directory) can be created by running:

$ raft.py setup --default

Note

Users installing with the --default option should ensure their working directory does not have unreasonable (e.g. < 1 TB) storage limitations.

Running the demonstration

The LENS demonstration provides an end-to-end example using a melanoma patient (Pt01) from the dataset associated with Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma (Hugo et al., 2016).

To run the demonstration, cd to your raft/ directory and run:

$ raft.py run-demo --workflow lens --version 1.9-dev

This will:

  • Create a project named demo-lens-v1.9-dev in ./raft/projects

  • Download the required RAFT modules

  • Download the demo references, sample-level FASTQs, and sample manifest

  • Run the project’s workflow

During execution, you will see progress messages such as:

Initializing project demo-lens...
Pulling off-the-shelf workflow...
This may take some time due to module fetching.
Loading manifest...
Loading references...
...
All human references downloaded successfully!
Loading fastqs...
Building workflow...
Connecting subworkflows...
Populating default parameters...
Running workflow...

The resulting project will be stored in /path/to/raft/projects/demo-lens-v1.9-dev/.

What’s next?

After the demonstration completes: