diff --git a/Readme.md b/Readme.md index 6237aed..da71c39 100644 --- a/Readme.md +++ b/Readme.md @@ -6,13 +6,13 @@ Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zu ## Prequisites -0. This project requires python 3.6 or higher. Please check your version with +1. This project requires python 3.6 or higher. Please check your version with ```bash $ python --version ``` -1. It is also a good idea to set up a venv +2. It is also a good idea to set up a venv ```bash python -m venv .cellxgene-gateway @@ -33,31 +33,6 @@ pip install git+https://github.com/Novartis/cellxgene-gateway # NOT YET DONE, COMING! STAY TUNED ``` -### Option 3: Developer Install - -If you want to develop the code, you will need to clone the repo. - -1. Clone the repo - -```bash - git clone https://github.com/Novartis/cellxgene-gateway.git - cd cellxgene-gateway -``` - -2. Install requirements with - -```bash -pip install -r requirements.txt -``` - -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. Prepare a folder with .h5ad files, for example @@ -71,8 +46,8 @@ wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc 2. Set your environment variables correctly: ```bash -export CELLXGENE_LOCATION=`which cellxgene` export CELLXGENE_DATA=../cellxgene_data # change this directory if you put data in a different place. +export CELLXGENE_LOCATION=`which cellxgene` export GATEWAY_HOST=localhost:5005 export GATEWAY_PROTOCOL=http export GATEWAY_IP=127.0.0.1 @@ -106,6 +81,31 @@ Currently we use a build.sh that copies the gateway to a "build" directory befor # Development +## Developer Install + +If you want to develop the code, you will need to clone the repo. Make sure you have the prequesite listed above, then: + +1. Clone the repo + +```bash + git clone https://github.com/Novartis/cellxgene-gateway.git + cd cellxgene-gateway +``` + +2. Install requirements with + +```bash +pip install -r requirements.txt +``` + +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 Linters pip install isort flake8 black diff --git a/cellxgene_gateway/templates/filecrawl.html b/cellxgene_gateway/templates/filecrawl.html index acdf372..a52ef25 100644 --- a/cellxgene_gateway/templates/filecrawl.html +++ b/cellxgene_gateway/templates/filecrawl.html @@ -25,7 +25,7 @@
-

Please wait until a dataset is done loading before trying to launch a different one

+

Please click on a dataset to view it in Cellxgene Server.


{{ rendered_html|safe }} diff --git a/run.sh.example b/run.sh.example index cb59098..095f57a 100644 --- a/run.sh.example +++ b/run.sh.example @@ -6,4 +6,4 @@ export GATEWAY_PROTOCOL=http export GATEWAY_IP=127.0.0.1 #Once these are set, you run like a normal Flask app -python gateway.py +cellxgene-gateway