Covid_TA_cellxgene_install

Installation instructions for COVID TA project

Modeling after Angela Pisco's tutorial: https://github.com/czbiohub/cellxgene-training

Cellxgene documentation for reference: https://chanzuckerberg.github.io/cellxgene/posts/install

Make sure you have Google Chrome working on your computer

Assuming you're working from a clean MacOS environment:

1. Install Anaconda

Download: https://www.anaconda.com/products/individual

Installation instructions: https://docs.anaconda.com/anaconda/install/mac-os/

2. Open terminal

Spotlight search (command+space bar): terminal

3. Install python dependencies

pip install scanpy

pip install louvain

4. Install cellxgene

pip install cellxgene

5. Download h5ad files:

https://drive.google.com/drive/u/0/folders/1rCXJjCX5fN2_7YH2k-hmjGF7WUGEbo3Q

Save .h5ad files to your folder of choice. This folder will contain your annotations from cellxgene so make sure you know where it is!

6. Navigate to folder where you have saved .h5ad files and open h5ad in cellxgene

This is the step you will do every time you want to use cellxgene

For example, if my .h5ad is in ~/Documents/COVID_TA:

cd ~/Documents/COVID_TA

cellxgene launch [path-to-your-object/name-object.h5ad] --experimental-enable-reembedding --open

Trick to launch h5ad if you don't know the specific path:

Open a finder window right next to the terminal window. Select the h5ad file in finder and drag it to terminal.

Any annotations you make in cellxgene will save in a csv file in your working directory and then we can merge the annotations back into the object afterwards.

7. Close cellxgene when finished!

press ctrl+c