---
title: Install
subtitle: Install
layout: default
---
# Installing cellxgene

Cellxgene has two parts:
* [`cellxgene`](launch) is the main explorer application, which takes an already-processed `h5ad` file as input. This is installed by default.  
* [`cellxgene prepare`](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