SVRare-js

This is an app to take the resulting sqlite db from SVRare-db and visualise the data using React and Expressjs

Install

yarn to install dependencies. Works with node V17.2.0.

One can use nvm to manage different versions of node.

Customise environment

Edit .env to setup the environment. The React app will run on PORT, and the server will run on SERVER_PORT. PUBLIC_PATH is where bam/vcf files are stored. I usually use sshfs to mount a remote server where the files are stored. The bam/vcf files are used to visualise structural variants using igv.js Since the bam/vcf files will be served with Expressjs, the path will need modification, by replacing /path/to/files with http://localhost:9000/files. In this case, you can assign /path/to/ to PATH_REPLACE_ORIGIN, and http://localhost:9000/ to PATH_REPLACE_ORIGIN.

Deploy app

Simply run yarn build. You can also run yarn run start to run in development mode. However in this case the app will use .env.local instead of .env for setting up environment

Optional

In case you have a different database makeup, use squelize-auto to help generate models ./node_modules/sequelize-auto/bin/sequelize-auto -d data/svrare.sqlite -e sqlite -l ts -c src/config/database.config.ts -o src/model

Large bam / vcf files stored remotely

To load large bam / vcf files remotely, people usually use sshfs.

sshfs on Mac

Recently macfuse stopped being open source, so brewing becomes an issue. Work around:

brew install --cask macfuse

brew install gromgit/fuse/sshfs-mac

Caveats

All caveats come with pedigreejs.

• Unless directly rendering pedigree from a .ped file, a node without parents, but not on the top level, will produce an error. But using .ped file lacks the support of extra node annotations (such as data not available etc). So the app reads .ped files, and process it. For this approach to work, just give those nodes dummy parents. Dummy parents won't show up if noparents is true.
• pedigreejs relies on jquery, and its use of the $ sign is not natively supported by react-scripts. My workaround is to add a plugin to the webpack.config.*.js to let react-scripts recognise $ (stored in asset), and copy the files to the node_modules.