@milaboratories/biowasm-tools

Biowasm Tools

This package provides pre-bundled genomics tools, enabling offline usage. Currently, it includes kalign.

Aioli

Aioli is a library for running genomics command-line tools in the browser using WebAssembly. See Who uses biowasm for example use cases.

Getting started

• Documentation
• List of supported packages

Development

Setup

Run npm install to install dependencies.

Then run npm run dev to launch the web server and use src/example.js as a sample web app that uses the dev version of Aioli.

Tests

Run npm run test.

Deploy a new release candidate

• Update version in package.json (append -rc1 for release candidates)
• Build: npm run build
• Create npm package: npm pack
• Publish package: npm publish [tgzfile] --tag next
• To use pre-release version: npm install @biowasm/aioli@next

Deploy a new version

• Update version in package.json
• Build: npm run build
• Publish package: npm publish --access public
• Create release in the GitHub repo
• Add to biowasm.json
• Deploy biowasm CDN with env=stg, tool=aioli and run biowasm tests to validate that stg tests still pass
• Repeat with env=prd

Architecture

• Aioli creates a single WebWorker, in which all WebAssembly tools run.
• We use a PROXYFS virtual filesystem so we can share a filesystem across all WebAssembly modules, i.e. the output of one tool can be used as the input of another tool.
• We use a WORKERFS virtual filesystem to mount local files efficiently (i.e. without having to load all their contents into memory). To support use cases where tools need to create files in the same folder as those ready-only files (e.g. samtools index), we automatically create a symlink from each local file's WORKERFS path to a path in PROXYFS.
• Once the WebWorker initializes, it loads the WebAssembly modules one at a time. To support this, we need to encapsulate each module using Emscripten's -s MODULARIZE=1, i.e. the .js file will contain a Module function that initializes the module and returns a Promise that resolves when the module is loaded.
• We do WebAssembly feature detection at initialization using wasm-feature-detect. If a tool needs WebAssembly SIMD and the user has a browser that does not support it, we will load the non-SIMD version of that tool.
• We communicate with the WebWorker using the Comlink library.

Background info

What is WebAssembly?

WebAssembly is a fast, low-level, compiled binary instruction format that runs in all major browsers at near native speeds. One key feature of WebAssembly is code reuse: you can port existing C/C++/Rust/etc tools to WebAssembly so those tools can run in the browser.

What is a WebWorker?

WebWorkers allow you to run JavaScript in the browser in a background thread, which keeps the browser responsive.

Compiling into WebAssembly

See the biowasm project.