update readme

Readme.md

@@ -4,6 +4,8 @@ Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zu
 
 ## Running locally
 
+We assume your current working directory is the directory into which you've cloned this repository.
+
 0. This project requires python 3.6 or higher. Please check your version with
 
 ```bash
@@ -23,6 +25,26 @@ source .cellxgene-gateway/bin/activate
 pip install -r requirements.txt
 ```
 
+1. 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
+```
+
 1. Prepare a folder with .h5ad files, for example
 
 ```bash
@@ -30,27 +52,33 @@ mkdir ../cellxgene_data
 wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
 ```
 
-1. Copy run.sh.example to run.sh:
+1. Set your environment variables correctly:
 
 ```bash
-cp run.sh.example run.sh
+export CELLXGENE_LOCATION=`which cellxgene`
+export CELLXGENE_DATA=../cellxgene_data  # change this directory if you put data in a different place.
+export GATEWAY_HOST=localhost:5005
+export GATEWAY_PROTOCOL=http
+export GATEWAY_IP=127.0.0.1
 ```
 
-`run.sh` defines various environment variables:
+1. Now, execute the cellxgene gateway:
 
-* `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
+```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`
+* `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.
+The defaults should be fine if you set up a venv and cellxgene_data folder as above.
 
-1. Finally, execute run.sh:
-
-```
-source run.sh
-```
 
 # Customization
 
@@ -63,29 +91,23 @@ The current paradigm for customization is to modify files during a build or depl
 
 Currently we use a build.sh that copies the gateway to a "build" directory before modifying with sed and the like.
 
-# Development #
+# Development
 
-## Running Linters ##
+## Running Linters
 
 pip install isort flake8 black
 
-```
+```bash
 isort -rc .
-```
-
-```
 flake8 .
+black -l 79 .
 ```
 
-```
-black .
-```
-
-# Getting Help #
+# Getting Help
 
 If you need help for any reason, please make a github ticket. One of the contributors should help you out.
 
-# Contributors #
+# Contributors
 
 * Niket Patel - https://github.com/NiketPatel9
 * Alok Saldanha - https://github.com/alokito

cellxgene_gateway.egg-info/PKG-INFO

@@ -1,12 +0,0 @@
-Metadata-Version: 1.1
-Name: cellxgene-gateway
-Version: 0.1
-Summary: Cell-by-gene Gateway
-Home-page: http://github.com/Novartis/cellxgene-gateway
-Author: Niket Patel, Yohann Potier, Alok Saldanha
-Author-email: alok.saldanha@novartis.com
-License: MIT
-Description: UNKNOWN
-Keywords: visualization,genomics
-Platform: UNKNOWN
-Classifier: Topic :: Scientific/Engineering :: Visualization

cellxgene_gateway.egg-info/SOURCES.txt

@@ -1,20 +0,0 @@
-setup.py
-cellxgene_gateway/__init__.py
-cellxgene_gateway/backend_cache.py
-cellxgene_gateway/cache_entry.py
-cellxgene_gateway/cellxgene_exception.py
-cellxgene_gateway/dir_util.py
-cellxgene_gateway/env.py
-cellxgene_gateway/extra_scripts.py
-cellxgene_gateway/gateway.py
-cellxgene_gateway/path_util.py
-cellxgene_gateway/process_exception.py
-cellxgene_gateway/prune_process_cache.py
-cellxgene_gateway/subprocess_backend.py
-cellxgene_gateway/util.py
-cellxgene_gateway.egg-info/PKG-INFO
-cellxgene_gateway.egg-info/SOURCES.txt
-cellxgene_gateway.egg-info/dependency_links.txt
-cellxgene_gateway.egg-info/entry_points.txt
-cellxgene_gateway.egg-info/requires.txt
-cellxgene_gateway.egg-info/top_level.txt

cellxgene_gateway.egg-info/dependency_links.txt

@@ -1 +0,0 @@
-

cellxgene_gateway.egg-info/entry_points.txt

@@ -1,3 +0,0 @@
-[console_scripts]
-cellxgene-gateway = cellxgene_gateway.gateway:main
-

cellxgene_gateway.egg-info/requires.txt

@@ -1,5 +0,0 @@
-cellxgene
-flask
-flask_api
-psutil
-requests

cellxgene_gateway.egg-info/top_level.txt

@@ -1 +0,0 @@
-cellxgene_gateway