Aioli

Aioli is a framework for building fast genomics web tools by compiling existing C/C++ command-line tools into WebAssembly and running them in background threads in the browser using WebWorkers.

For an example of what can be built with Aioli, see fastq.bio, which was built by compiling seqtk to WebAssembly, and yielded significant speedups. fastq.bio uses Aioli to manage the WebAssembly calls and communications between the main thread and the WebWorker.

Tools that use Aioli

fastq.bio
bam.bio
genomeribbon.com (work in progress)

Getting Started

What is WebAssembly?

WebAssembly is a very fast, low-level, compiled binary instruction format that runs in all major browsers at near native speeds.

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

Download the Emscriptem SDK
Follow the Emscriptem tutorial for details on how to compile C/C++ files into app.js and app.wasm.
Use template.html as a starting point for building your app. Built on top of Aioli, this simple app allows users to specify a local file to parse (URLs + drag & drop supported), and will mount that file to a virtual file system inside a WebWorker, sample that file randomly, run a WebAssembly command on each chunk inside the WebWorker, track its output, and display progress throughout.
You can install Aioli as a JavaScript package through npm: npm install @robertaboukhalil/aioli.

Structure

aioli.js

Main Aioli class

// Example from fastq.bio:
// Create Aioli object and import the compiled .js file
this.aioli = new Aioli({
    imports: [ "seqtk.js" ]
});

// Initialize Aioli. This will launch the WebWorker and set up a virtual File System
this.aioli.init().then(() => {
    console.log("Aioli Initialized");

    // Mount a File object to the virtual file system within the WebWorker
    return this.aioli.mount({
        files: [ myFile ]
    });
}).then(() => {
    // Launch main() function with command-line arguments "comp" and the File object
    return this.aioli.exec({
        args: ["comp", myFile],
    });
}).then(d => {
    // Once it's done running, retrieve the output
    console.log(d);
});

aioli.user.js

Custom user functions. Modify this file to allow the WebWorker to call custom functions you wrote (can't directly pass functions from main thread to WebWorker).

aioli.worker.js

Code that runs inside a WebWorker. Should not need modifying unless you are adding features.

richardgoater/aioli