refactor to allow use with console entry points

Readme.md

@@ -1,50 +1,58 @@
-# Overview #
+# Overview
 
 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
 
 0. This project requires python 3.6 or higher. Please check your version with
 
-    python --version
+```bash
+$ python --version
+```
 
 1. Set up a venv with
-```
+
+```bash
 python -m venv .cellxgene-gateway
 source .cellxgene-gateway/bin/activate
 ```
 
-2. Install requirements with
-```
+1. Install requirements with
+
+```bash
 pip install -r requirements.txt
 ```
-3. Prepare a folder with .h5ad files, for example
 
-```
-mkdir cellxgene_data
+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
 ```
 
-4. Copy run.sh.example to run.sh:
-```
+1. Copy run.sh.example to run.sh:
+
+```bash
 cp run.sh.example run.sh
 ```
+
 `run.sh` defines various environment variables:
 
-* DEPLOYMENT_ENV - expects 'dev', 'tst' or 'prd'
-* CELLXGENE_LOCATION - the location of the cellxgene executable, e.g. ~/anaconda2/envs/cellxgene/bin/cellxgene
-* CELLXGENE_DATA - a directory that can contain subdirectories with .h5ad data files, *without* trailing slash, e.g. /mnt/cellxgene_data
-* GATEWAY_HOST - the hostname and port that the gateway will run on, typically localhost:5005 if running locally
-* GATEWAY_PROTOCOL - typically http when running locally, can be https when deployed if the gateway is behind a load balancer or reverse proxy.
+* `DEPLOYMENT_ENV` - expects 'dev', 'tst' or 'prd'
+* `CELLXGENE_LOCATION` - the location of the cellxgene executable, e.g. ~/anaconda2/envs/cellxgene/bin/cellxgene
+* `CELLXGENE_DATA` - a directory that can contain subdirectories with .h5ad data files, *without* trailing slash, e.g. /mnt/cellxgene_data
+* `GATEWAY_HOST` - the hostname and port that the gateway will run on, typically localhost:5005 if running locally
+* `GATEWAY_PROTOCOL` - typically http when running locally, can be https when deployed if the gateway is behind a load balancer or reverse proxy.
 
 The defaults should be fine if you set up  a venv and cellxgene_data folder as above.
 
-5. Finally, execute run.sh:
+1. Finally, execute run.sh:
+
 ```
 source run.sh
 ```
 
-# Customization #
+# Customization
 
 The current paradigm for customization is to modify files during a build or deployment phase: