cellxgene/docs/posts/install.md

title, subtitle, layout

title	subtitle	layout
Install	Install	default

Installing cellxgene

Cellxgene has two parts:

• cellxgene is the main explorer application, which takes an already-processed h5ad file as input. This is installed by default.
• cellxgene prepare provides auxiliary functionality for preparing your dataset. This is not installed by default.

Requirements

You'll need python 3.6+ and Google Chrome. The web UI is tested on OSX and Windows using Chrome, and the python CLI is tested on OSX and Ubuntu (via WSL/Windows). It should work on other platforms, but if you run into trouble let us know.

Basic install

To install cellxgene alone, run:
pip install cellxgene

To install cellxgene and the optional cellxgene prepare, run:
pip install cellxgene[prepare]

Note: if the aforementioned optional prepare package installation fails, you can also install these packages directly:

pip install scanpy>=1.3.7 python-igraph louvain>=0.6

Using a conda environment

To install cellxgene alone, run:

conda create --yes -n cellxgene python=3.7
conda activate cellxgene
pip install cellxgene

To install cellxgene and the optional cellxgene prepare, run:

conda create --yes -n cellxgene python=3.7
conda activate cellxgene
pip install cellxgene[prepare]

Using a virtual environment

To install cellxgene alone, run:

ENV_NAME=cellxgene
python3.7 -m venv ${ENV_NAME}
source ${ENV_NAME}/bin/activate
pip install cellxgene

To install cellxgene and cellxgene prepare, run:

ENV_NAME=cellxgene
python3.7 -m venv ${ENV_NAME}
source ${ENV_NAME}/bin/activate
pip install cellxgene[prepare]

Using docker

Build the image
docker build . -t cellxgene

Run the container and mount data
docker run -v "$PWD/example-dataset/:/data/" -p 5005:5005 cellxgene launch --host 0.0.0.0 data/pbmc3k.h5ad

You will need to use --host 0.0.0.0 to have the container listen to incoming requests from the browser