diff --git a/Readme.md b/Readme.md index 9cb4179..6d8b9ac 100644 --- a/Readme.md +++ b/Readme.md @@ -2,9 +2,9 @@ Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets. It displays an index of available h5ad (anndata) files. When a user clicks on a file name, it launches a Cellxgene Server instance that loads that particular data file and once it is available proxies requests to that server. -## Running locally +# Running locally -We assume your current working directory is the directory into which you've cloned this repository. +## Prequisites 0. This project requires python 3.6 or higher. Please check your version with @@ -12,47 +12,53 @@ We assume your current working directory is the directory into which you've clon $ python --version ``` -1. Set up a venv with +1. It is also a good idea to always set up a venv. ```bash python -m venv .cellxgene-gateway source .cellxgene-gateway/bin/activate ``` -2. Install requirements with - -```bash -pip install -r requirements.txt -``` - -3. Install the gateway: - -_To install in development mode:_ - -```bash -python setup.py develop -``` - -_To install from GitHub:_ - -```bash -pip install git+https://github.com/Novartis/cellxgene-gateway -``` - -_To install from PyPI:_ - -```bash -# NOT YET DONE, COMING! STAY TUNED -``` - -4. Prepare a folder with .h5ad files, for example +2. Prepare a folder with .h5ad files, for example ```bash mkdir ../cellxgene_data wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad ``` -5. Set your environment variables correctly: + +## Pip Install from Github + +```bash +pip install git+https://github.com/Novartis/cellxgene-gateway +``` + +### Install from PyPI + +```bash +# NOT YET DONE, COMING! STAY TUNED +``` + +### Developer Install + +If you want to develop the code, you will need to clone the repo. We assume your current working directory is the directory into which you've cloned this repository. + + +1. Install requirements with + +```bash +pip install -r requirements.txt +``` + +2. Install the gateway in developer mode + +```bash +python setup.py develop +``` + +## Running cellxgene gateway + +1. Set your environment variables correctly: ```bash export CELLXGENE_LOCATION=`which cellxgene` @@ -62,7 +68,7 @@ export GATEWAY_PROTOCOL=http export GATEWAY_IP=127.0.0.1 ``` -6. Now, execute the cellxgene gateway: +2. Now, execute the cellxgene gateway: ```bash cellxgene-gateway