Installing RAFT

RAFT is the Nextflow-based workflow manager used to run the LENS workflow.

Users should refer to the RAFT readthedocs.org page for the latest information, but we have provided a brief overview for install RAFT below.

Installing through Conda

Users should ensure Conda is installed prior to install RAFT. Users can find installation instructions on the Conda documentation page.

To install RAFT using Conda, run:

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

Installing through pip

Installing RAFT through pip will require users to separately install Apptainer and Git.

To install RAFT using pip, run:

$ 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).

Setup

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

Users 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 the following command in the terminal:

$ 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.

At this point, RAFT is installed and users are ready to run the LENS workflow.