Installation

Manual Installation

The recommended installation is as follows. Create a conda environment and activate it:

$ conda create -n CellBender python=3.7
$ source activate CellBender

Install the pytables module:

(CellBender) $ conda install -c anaconda pytables

Install pytorch (shown below for CPU; if you have a CUDA-ready GPU, please skip this part and follow these instructions instead):

(CellBender) $ conda install pytorch torchvision -c pytorch

Clone this repository and install CellBender:

(CellBender) $ git clone https://github.com/broadinstitute/CellBender.git
(CellBender) $ pip install -e CellBender

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:0.1.0

Terra Workflow

For Terra users, the following workflow is publicly available: