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separated different ways of running locally

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Alokito
2019-09-06 14:26:00 -04:00
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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