Unverified Commit e142c625 authored by Alokito's avatar Alokito Committed by GitHub
Browse files

separated different ways of running locally

parent ec0bf625
......@@ -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
2. Prepare a folder with .h5ad files, for example
```bash
pip install -r requirements.txt
mkdir ../cellxgene_data
wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
```
3. Install the gateway:
_To install in development mode:_
## Pip Install from Github
```bash
python setup.py develop
pip install git+https://github.com/Novartis/cellxgene-gateway
```
_To install from GitHub:_
### Install from PyPI
```bash
pip install git+https://github.com/Novartis/cellxgene-gateway
# NOT YET DONE, COMING! STAY TUNED
```
_To install from PyPI:_
### 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
# NOT YET DONE, COMING! STAY TUNED
pip install -r requirements.txt
```
4. Prepare a folder with .h5ad files, for example
2. Install the gateway in developer mode
```bash
mkdir ../cellxgene_data
wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
python setup.py develop
```
5. Set your environment variables correctly:
## 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
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment