Aioli
Aioli is a framework for building fast genomics web tools using WebAssembly and WebWorkers.
Tools that use Aioli
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
- 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.
