Commit 6183a7ed authored by Alok Saldanha's avatar Alok Saldanha
Browse files

streamlined normal example, readme docs

parent 20bffbfc
......@@ -6,13 +6,13 @@ Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zu
## Prequisites
0. This project requires python 3.6 or higher. Please check your version with
1. This project requires python 3.6 or higher. Please check your version with
```bash
$ python --version
```
1. It is also a good idea to set up a venv
2. It is also a good idea to set up a venv
```bash
python -m venv .cellxgene-gateway
......@@ -33,31 +33,6 @@ pip install git+https://github.com/Novartis/cellxgene-gateway
# NOT YET DONE, COMING! STAY TUNED
```
### Option 3: Developer Install
If you want to develop the code, you will need to clone the repo.
1. Clone the repo
```bash
git clone https://github.com/Novartis/cellxgene-gateway.git
cd cellxgene-gateway
```
2. Install requirements with
```bash
pip install -r requirements.txt
```
3. Install the gateway in developer mode
```bash
python setup.py develop
```
For convenience, the code repo includes a `run.sh.example` shell script to run the gateway.
## Running cellxgene gateway
1. Prepare a folder with .h5ad files, for example
......@@ -71,8 +46,8 @@ wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc
2. Set your environment variables correctly:
```bash
export CELLXGENE_LOCATION=`which cellxgene`
export CELLXGENE_DATA=../cellxgene_data # change this directory if you put data in a different place.
export CELLXGENE_LOCATION=`which cellxgene`
export GATEWAY_HOST=localhost:5005
export GATEWAY_PROTOCOL=http
export GATEWAY_IP=127.0.0.1
......@@ -106,6 +81,31 @@ Currently we use a build.sh that copies the gateway to a "build" directory befor
# Development
## Developer Install
If you want to develop the code, you will need to clone the repo. Make sure you have the prequesite listed above, then:
1. Clone the repo
```bash
git clone https://github.com/Novartis/cellxgene-gateway.git
cd cellxgene-gateway
```
2. Install requirements with
```bash
pip install -r requirements.txt
```
3. Install the gateway in developer mode
```bash
python setup.py develop
```
For convenience, the code repo includes a `run.sh.example` shell script to run the gateway.
## Running Linters
pip install isort flake8 black
......
......@@ -25,7 +25,7 @@
</header>
<br>
<h4>Please wait until a dataset is done loading before trying to launch a different one</h4>
<h4>Please click on a dataset to view it in Cellxgene Server.</h4>
<br>
{{ rendered_html|safe }}
......
......@@ -6,4 +6,4 @@ export GATEWAY_PROTOCOL=http
export GATEWAY_IP=127.0.0.1
#Once these are set, you run like a normal Flask app
python gateway.py
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