Merge pull request #24 from biowasm/v2

Aioli v2

.gitignore

@@ -0,0 +1,4 @@
+.DS_Store
+node_modules
+dist
+package-lock.json

README.md

@@ -2,38 +2,41 @@
 
 [![npm](https://img.shields.io/npm/v/@biowasm/aioli)](https://www.npmjs.com/package/@biowasm/aioli)
 
-Aioli is a framework for building fast genomics web applications using [WebAssembly](https://developer.mozilla.org/en-US/docs/WebAssembly) and [WebWorkers](https://developer.mozilla.org/en-US/docs/Web/API/Web_Workers_API).
+Aioli is a library for running genomics command-line tools in the browser using WebAssembly. The WebAssembly modules are obtained from the [biowasm](https://github.com/biowasm/biowasm) CDN.
 
-## Tools using Aioli
-
-| Tool | URL | Repo |
-|-|-|-|
-| Ribbon | [genomeribbon.com](https://genomeribbon.com) | [MariaNattestad/Ribbon](https://github.com/MariaNattestad/Ribbon) |
-| Alignment Sandbox | [alignment.sandbox.bio](https://alignment.sandbox.bio/) | [RobertAboukhalil/alignment-sandbox](https://github.com/robertaboukhalil/alignment-sandbox) |
-| fastq.bio | [fastq.bio](http://www.fastq.bio/) | [RobertAboukhalil/fastq.bio](https://github.com/robertaboukhalil/fastq.bio) |
-| bam.bio | [bam.bio](http://www.bam.bio/) | [RobertAboukhalil/bam.bio](https://github.com/robertaboukhalil/bam.bio) |
 
 ## Getting Started
 
-As shown below, **you can obtain Aioli from our biowasm CDN**, or you can install it from npm: `npm install @biowasm/aioli` (use the `npm` option if you need to host the Aioli module locally).
-
 ### A simple example
 
-Here's Aioli in action running the genomics tool `samtools` on a small `SAM` file:
+Running the genomics tool `samtools` on a small file:
+
+```html
+<script src="https://cdn.biowasm.com/v2/aioli/latest/aioli.js"></script>
+<script type="module">
+// Note that we use `script type="module"` so we can use top-level await statements
+const CLI = await new Aioli("samtools/1.10");
+const output = await CLI.exec("samtools view -q 20 /samtools/examples/toy.sam");
+console.log(output);
+</script>
+```
+
+### Load multiple tools
+
+Aioli supports running multiple bioinformatics tools at once:
 
 ```html
-<script src="https://cdn.biowasm.com/aioli/latest/aioli.js"></script>
-<script>
-let samtools = new Aioli("samtools/1.10");
-
-document.write("Loading...");
-samtools
-    // Initialize samtools
-    .init()
-    // Run "samtools view" command with "-q 20" filter
-    .then(() => samtools.exec("view -q 20 /samtools/examples/toy.sam"))
-    // Output result
-    .then(d => document.write(`<pre>${d.stdout}\n${d.stderr}</pre>`));
+<script src="https://cdn.biowasm.com/v2/aioli/latest/aioli.js"></script>
+<script type="module">
+const CLI = await new Aioli(["samtools/1.10", "seqtk/1.2"]);
+
+// Run "samtools view"
+let output = await CLI.exec("samtools view -q 20 /samtools/examples/toy.sam");
+console.log(output);
+
+// Run "seqtk" to get the help screen
+output = await CLI.exec("seqtk");
+console.log(output);
 </script>
 ```
 
@@ -44,29 +47,24 @@ We can update the previous example to run `samtools` on a file provided by the u
 ```html
 <input id="myfile" type="file" multiple>
 
-<script src="https://cdn.biowasm.com/aioli/latest/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(f => samtools.exec(`view -q20 ${f.path}`))
-        // Capture output
-        .then(d => console.log(d.stdout));
+<script src="https://cdn.biowasm.com/v2/aioli/latest/aioli.js"></script>
+<script type="module">
+const CLI = await new Aioli("samtools/1.10");
+const output = await CLI.exec("samtools --version-only");
+console.log(`Loaded ${output}`);
+
+// Get the SAM file header when user selects a file from their computer
+async function runSamtools(event) {
+    // First, mount the file(s) to a virtual file system
+    const files = event.target.files;
+    await CLI.mount(files);
+
+    // Retrieve SAM header on the first file the user selected
+    const output = await CLI.exec(`samtools view -H ${files[0].name}`);
+    console.log(output);
 }
-document.getElementById("myfile").addEventListener("change", loadFile, false);
+
+document.getElementById("myfile").addEventListener("change", runSamtools, false);
 </script>
 ```
 
@@ -80,23 +78,19 @@ document.getElementById("myfile").addEventListener("change", loadFile, false);
 // Format: <module>/<version>
 // -------------------------------------
 
-// Retrieve specific version (recommended for stability)
 new Aioli("seqtk/1.2");
-
-// Retrieve latest version
-new Aioli("seqtk/latest");
-
+new Aioli("samtools/1.10");
 
 // -------------------------------------
 // Format: <module>/<program>/<version>
 // -------------------------------------
 
 // For most bioinformatics tools, <module> == <program>
-new Aioli("seqtk/seqtk/1.2");
+new Aioli("seqtk/seqtk/1.2");  // seqtk/1.2 == seqtk/seqtk/1.2
 
 // But not always! Some tools have multiple sub-tools
-new Aioli("seq-align/smith_waterman/1.2");
-new Aioli("seq-align/needleman_wunsch/1.2");
+new Aioli("seq-align/smith_waterman/2017.10.18");
+new Aioli("seq-align/needleman_wunsch/2017.10.18");
 ```
 
 ### Advanced
@@ -105,14 +99,25 @@ By default, Aioli retrieves the `.wasm` modules and the Aioli WebWorker code fro
 
 ```javascript
 new Aioli({
-    module: "seq-align",
-    program: "smith_waterman",              // optional (defaults to $module)
-    version: "latest",                      // optional (defaults to latest)
-    urlModule: "./path/to/wasm/files/",     // optional (defaults to biowasm CDN)
+    tool: "seq-align",
+    version: "2017.10.18",
+    program: "smith_waterman",              // optional (defaults to "tool" name)
+    urlPrefix: "./path/to/wasm/files/",     // optional (defaults to biowasm CDN)
+}, {
     urlAioli: "./path/to/aioli.worker.js",  // optional (defaults to biowasm CDN)
 });
 ```
 
+## Tools using Aioli
+
+| Tool | URL | Repo |
+|-|-|-|
+| Ribbon | [genomeribbon.com](https://genomeribbon.com) | [MariaNattestad/Ribbon](https://github.com/MariaNattestad/Ribbon) |
+| Alignment Sandbox | [alignment.sandbox.bio](https://alignment.sandbox.bio/) | [RobertAboukhalil/alignment-sandbox](https://github.com/robertaboukhalil/alignment-sandbox) |
+| fastq.bio | [fastq.bio](http://www.fastq.bio/) | [RobertAboukhalil/fastq.bio](https://github.com/robertaboukhalil/fastq.bio) |
+| bam.bio | [bam.bio](http://www.bam.bio/) | [RobertAboukhalil/bam.bio](https://github.com/robertaboukhalil/bam.bio) |
+
+
 ## Background info
 
 ### What is WebAssembly?