Installation

Prerequisites

raft requires that singularity (currently known as apptainer) be installed. singularity is used for downloading reference files. Users may still use other containerization tools (e.g. docker) within raft.

Installing through Conda

To install RAFT using Conda, run:

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

Installing through pip

To install RAFT using pip (recommmended), 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 also contains the RAFT configuration file. To set up RAFT, run:

$ raft.py setup

This will prompt the user to provide paths for each require subdirectory while providing a sensible defeault. This is useful for putting directories that will containlarge files (e.g. /Projects) on a storage device with sufficient storage. The resulting subdirectory within the RAFT setup directory will be a symlink to the user-specified directory.

Users that want the default setup in which all RAFT subdirectories are created in their current working directory can run:

$ raft.py setup -d