cell-atlas

This is the front-end for the UCSC's Cell Atlas. It does handy things like exposing single cell clustering solutions to the community via a RESTful api, and stores the Cell Type Worksheets of our users. Check out the back-end for Cell Type Worksheets.

The associated git code repositories are:

Stuartlab-UCSC/cell-atlas the server that serves the HTML and javascript for the web pages

Stuartlab-UCSC/cluster-db the server of the data as well as handling user logins

Stuartlab-UCSC/ctwpy the scripts to ingest scanpy objects or TSV files into the cell type workbench

Stuartlab-UCSC/ctwseurat the scripts to ingest seurat objects into the cell type workbench

Stuartlab-UCSC/ctwingest a dependency of ctwpy and ctwseurat and contains the common code to ingest scanpy objects, seurat objects or TSV files into the cell type workbench

Requirements

node >= v10.16, git

Install

git clone https://github.com/stuartlab-UCSC/cell-atlas.git
cd cell-atlas
npm install

Start on development machine

npm start

Install on production

On your development machine, after modifying bin/deployWww to match your instance.

cd cell-atlas
bin/deployWww

On your production machine, after modifying bin/installWww to match your instance. Copy the script, bin/installWww into your install directory.

cd <install-dir>
installWww

Start on production machine

cd cell-atlas
bin/start

Stop on production machine

Find the process ID of the server and kill it.

ps -eaf | grep "node server.js"
kill <pid>

Code size view

To run source-map-explorer insert this in package.json, "dependencies" section:

source-map-explorer": "^1.5.0",

This was removed from the normal build because it causes an npm audit warning on its use of insecure 'open'.

Eslint all js files

cell-atlas/eslintAll

Code style guidelines

• use material-ui
• use 4 spaces for tabs