Installation

Via pip

Python packages can be conveniently installed from the Python Package Index (PyPI) using pip install. CellBender is available on PyPI and can be installed via

$ pip install cellbender

If your machine has a GPU with appropriate drivers installed, it should be automatically detected, and the appropriate version of PyTorch with CUDA support should automatically be downloaded as a CellBender dependency.

We recommend installing CellBender in its own conda environment. This allows for easier installation and prevents conflicts with any other python packages you may have installed.

$ conda create -n cellbender python=3.12
$ conda activate cellbender
(cellbender) $ pip install cellbender

Installation from source

Create a conda environment and activate it:

$ conda create -n cellbender python=3.12
$ conda activate cellbender

Clone this repository and install CellBender (in editable mode):

(cellbender) [~/] $ git clone https://github.com/broadinstitute/CellBender.git
(cellbender) [~/] $ cd CellBender
(cellbender) [~/CellBender] $ make install

If you prefer not to use the make command, you can also install CellBender from source via

(cellbender) [~/CellBender] $ pip install -e .

Install a specific commit directly from GitHub

This can be achieved via

(cellbender) $ pip install --no-cache-dir -U git+https://github.com/broadinstitute/CellBender.git@<SHA>

where <SHA> must be replaced by any reference to a particular git commit, such as a tag, a branch name, or a commit sha.

Docker Image

A GPU-enabled docker image is available from the Google Container Registry (GCR) as:

us.gcr.io/broad-dsde-methods/cellbender:latest

Older versions are available at the same location, for example as

us.gcr.io/broad-dsde-methods/cellbender:0.3.2

Terra Workflow

For Terra users (or any other users of WDL workflows), the following WDL workflow is publicly available:

cellbender/remove-background

Some documentation for the WDL is available at the above link, and some is visible on github.