@robertaboukhalil/aioli v1.1.0

Aioli

Aioli is a framework for building fast genomics web tools using WebAssembly and WebWorkers.

Tools that use Aioli

• fastq.bio
• bam.bio
• genomeribbon.com

Getting Started

Here is a simple example of Aioli in action running the genomics tool samtools on a user-provided file:

<input id="myfile" type="file" multiple>
<script src="aioli.js"></script>

<script>
let samtools = new Aioli("samtools/1.10");

// Initialize samtools and output the version
samtools
    .init()
    .then(() => samtools.exec("--version"))
    .then(d => console.log(d.stdout));

// When a user selects a .sam file from their computer,
// run `samtools view -q20` on the file
function loadFile(event)
{
    Aioli
        // First mount the file
        .mount(event.target.files[0])
        // Once it's mounted, run samtools view
        .then(file => samtools.exec(`view -q20 ${file.path}`))
        // Capture output
        .then(d => console.log(d.stdout));
}
document.getElementById("myfile").addEventListener("change", loadFile, false);
</script>

Background info

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

1. Download the Emscriptem SDK
2. Follow the Emscriptem tutorial for details on how to compile C/C++ files into app.js and app.wasm.
3. 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.
4. You can install Aioli as a JavaScript package through npm: npm install @robertaboukhalil/aioli.