Installation
Manual Installation
The recommended installation is as follows. Create a conda environment and activate it:
$ conda create -n CellBender python=3.7
$ conda 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: