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separated installing and running Cellxgene Gateway

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Alokito
2019-09-06 14:55:00 -04:00
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@@ -12,22 +12,16 @@ Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zu
$ python --version $ python --version
``` ```
1. It is also a good idea to always set up a venv. 1. It is also a good idea to set up a venv
```bash ```bash
python -m venv .cellxgene-gateway python -m venv .cellxgene-gateway
source .cellxgene-gateway/bin/activate source .cellxgene-gateway/bin/activate # type `deactivate` to deactivate the venv
``` ```
2. Prepare a folder with .h5ad files, for example ## Install cellxgene-gateway
```bash ### Pip Install from Github
mkdir ../cellxgene_data
wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
```
## Pip Install from Github
```bash ```bash
pip install git+https://github.com/Novartis/cellxgene-gateway pip install git+https://github.com/Novartis/cellxgene-gateway
@@ -41,24 +35,40 @@ pip install git+https://github.com/Novartis/cellxgene-gateway
### Developer Install ### 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. If you want to develop the code, you will need to clone the repo.
1. Clone the repo
1. Install requirements with ```bash
git clone https://github.com/Novartis/cellxgene-gateway.git
cd cellxgene-gateway
```
2. Install requirements with
```bash ```bash
pip install -r requirements.txt pip install -r requirements.txt
``` ```
2. Install the gateway in developer mode 3. Install the gateway in developer mode
```bash ```bash
python setup.py develop python setup.py develop
``` ```
For convenience, the code repo includes a `run.sh.example` shell script to run the gateway.
## Running cellxgene gateway ## Running cellxgene gateway
1. Set your environment variables correctly: 1. 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
```
2. Set your environment variables correctly:
```bash ```bash
export CELLXGENE_LOCATION=`which cellxgene` export CELLXGENE_LOCATION=`which cellxgene`
@@ -68,14 +78,12 @@ export GATEWAY_PROTOCOL=http
export GATEWAY_IP=127.0.0.1 export GATEWAY_IP=127.0.0.1
``` ```
2. Now, execute the cellxgene gateway: 3. Now, execute the cellxgene gateway:
```bash ```bash
cellxgene-gateway cellxgene-gateway
``` ```
For convenience, you can also change `run.sh.example` and execute it.
Here's what the environment variables mean: Here's what the environment variables mean:
* `CELLXGENE_LOCATION` - the location of the cellxgene executable, e.g. `~/anaconda2/envs/cellxgene/bin/cellxgene` * `CELLXGENE_LOCATION` - the location of the cellxgene executable, e.g. `~/anaconda2/envs/cellxgene/bin/cellxgene`