Installation

The recommended way to install nimble is via Docker, ensuring a consistent runtime environment without dependency conflicts.

Installing via Docker

To pull the latest nimble Docker image, run docker pull ghcr.io/bimberlab/nimble:latest

This will download the latest version of nimble with no further dependency or environment management.

Installing via Pip

Alternatively, nimble can be installed using pip. This requires Python 3 and samtools to be installed on your system. Currently, we support:

• macOS
• Linux distributions with musl support (e.g., Alpine, Debian/Ubuntu with the musl package)

To install nimble via pip, run pip install git+https://github.com/BimberLab/nimble

Verifying Installation

Verify that nimble is correctly installed by running:

docker run ghcr.io/bimberlab/nimble:latest -h

or, if you installed nimble with Python/pip:

python -m nimble -h

In either case, you should get output similar to:

usage: __main__.py [-h] [-v] {download,generate,align,report,plot} ...

nimble align

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

subcommands:
  {download,generate,align,report,plot}

Next steps

Once installed, proceed to the Quickstart Guide to learn how to use nimble for lightweight RNA-seq alignment.