Schematize

Visualization component of Pangenome Schematics for 1,000s of individuals and gigabase genomes.

Getting Started

git clone https://github.com/graph-genome/Schematize
cd Schematize
npm install
npm start

Open http://localhost:3000 to view it in the browser.

The page will reload if you make edits. You will also see any lint errors in the console.

Build

npm run build

Builds the app for production to the build folder. It correctly bundles React in production mode and optimizes the build for the best performance.

JBrowse2 Integration

((JBrowse2 integration is not done yet. If you'd like to contribute you can make a PR for Issue #7 ))

The whole code in this repository is integrated as a submodule in GMOD's JBrowse-Components. We are currently stashing our code @https://github.com/graph-genome/jbrowse-components/tree/pangenome_group_testing.

In order to get the plugin in JBrowse-Web to run, execute the following steps:

Clone the JBrowse-Components repository:

git clone --recurse-submodules -b pangenome_group_testing git@github.com:graph-genome/jbrowse-components.git

Install dependencies:

cd jbrowse-components/

yarn

Start the development server (it takes some time until it is up...):

(cd packages/jbrowse-web/ && yarn start)

Navigate to File -> New pangenome view. Now you have a PangenomeView track running in JBrowse2!

Developer Notes

All test files must be copied to jbrowse-components/packages/jbrowse-web/test_data. In jbrowse-components/packages/pangenome-view/src/PangenomeView/components/prototype/src/PangenomeSchematic.js change path data to path test_data so that we point to the currect folder for our data to load.