diff --git a/Readme.md b/Readme.md index 6d8b9ac..217d63f 100644 --- a/Readme.md +++ b/Readme.md @@ -12,22 +12,16 @@ Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zu $ 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 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 -mkdir ../cellxgene_data -wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad -``` - - -## Pip Install from Github +### Pip Install from Github ```bash pip install git+https://github.com/Novartis/cellxgene-gateway @@ -41,24 +35,40 @@ pip install git+https://github.com/Novartis/cellxgene-gateway ### 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 pip install -r requirements.txt ``` -2. Install the gateway in developer mode +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. 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 export CELLXGENE_LOCATION=`which cellxgene` @@ -68,14 +78,12 @@ export GATEWAY_PROTOCOL=http export GATEWAY_IP=127.0.0.1 ``` -2. Now, execute the cellxgene gateway: +3. Now, execute the cellxgene gateway: ```bash cellxgene-gateway ``` -For convenience, you can also change `run.sh.example` and execute it. - Here's what the environment variables mean: * `CELLXGENE_LOCATION` - the location of the cellxgene executable, e.g. `~/anaconda2/envs/cellxgene/bin/cellxgene`