mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-16 21:37:59 +08:00
110 lines
2.6 KiB
Markdown
110 lines
2.6 KiB
Markdown
---
|
|
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 an up-to-date version of **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.
|
|
|
|
[Python.org](https://www.python.org/downloads/) has help on installing a recent
|
|
version of Python, including the pip package manager. Chrome is available at
|
|
[Google.com/chrome](https://google.com/chrome).
|
|
|
|
## Basic install using pip
|
|
|
|
To install the `cellxgene` explorer 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
|
|
```
|
|
|
|
_On various Linux platforms, you may also need to install build dependencies first:_
|
|
|
|
```
|
|
sudo apt-get install build-essential python-dev
|
|
pip install scanpy>=1.3.7 python-igraph louvain>=0.6
|
|
```
|
|
|
|
If you already have `cellxgene` installed, you can update to the most recent version by running:
|
|
|
|
```
|
|
pip install cellxgene --upgrade
|
|
```
|
|
|
|
## 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 ${ENV_NAME}/bin/activate
|
|
pip install cellxgene[prepare]
|
|
```
|
|
|
|
## Using docker
|
|
|
|
Build the image
|
|
|
|
```
|
|
docker build . -t cellxgene
|
|
```
|
|
|
|
Run the container and mount data (change data location, `--port` and `--host` parameters as needed)
|
|
|
|
```
|
|
docker run -v "$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
|