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updated readme and run.sh.example to make getting started easier

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This commit is contained in:
Alok Saldanha
2019-09-04 15:25:29 -04:00
parent 52dd6dd156
commit 7fc9400b37
2 changed files with 21 additions and 14 deletions
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31
Readme.md
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@@ -4,22 +4,27 @@ Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zu
# Running locally #
Before running the gateway, make sure you can run the Cellxgene Server from CZI, and that you have a folder with h5ad files ready to view.
1. Set up a venv with
python -m venv .cellxgene-gateway
source .cellxgene-gateway/bin/activate
2. Install requirements with
pip install -r requirements.txt
3. Prepare a folder with .h5ad files, for example
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 and edit if you want to change venv or .h5ad folder position:
The first step is to set up an environment and install requirements:
```
# create an environment for packages
python -m venv .cellxgene-gateway
source .cellxgene-gateway/bin/activate
# install requirements
pip install -r requirements.txt
```
Then copy run.sh.example to run.sh and edit
```
cp run.sh.example run.sh
```
`run.sh` defines various environment variables, you probably only need to edit CELLXGENE_LOCATION and CELLXGENE_DATA:
`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
@@ -27,7 +32,9 @@ cp run.sh.example run.sh
* 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.
Finally, execute run.sh:
The defaults should be fine if you set up a venv and cellxgene_data folder as above.
5. Finally, execute run.sh:
```
source run.sh
```

4
run.sh.example
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@@ -1,5 +1,5 @@
export CELLXGENE_LOCATION=/path/to/cellxgene
export CELLXGENE_DATA=/path/to/datasets
export CELLXGENE_LOCATION=$(pwd)/.cellxgene-gateway/bin/cellxgene
export CELLXGENE_DATA=../cellxgene_data
export DEPLOYMENT_ENV=dev
export GATEWAY_HOST=localhost:5005
export GATEWAY_PROTOCOL=http