Liatir

Tauri 2 desktop runtime base for bioinformatics applications.

Provides a sandboxed WASM plugin system, a native sidecar abstraction, and a sequential pipeline orchestrator — ready to wire up real bio tools.

src-tauri/src/bridge/
  plugins.rs      ← WASM runtime (wasmtime + WASI p1). Full implementation.
  sidecar.rs      ← Native binary runner (tauri_plugin_shell). Scaffold.
  fs.rs           ← Sandboxed file system commands.
  ...             ← Other Tauri bridge modules (window, notifications, etc.)

src-ts/
  modules/rs/
    plugins/      ← TS bridge to the WASM runtime.
    sidecar/      ← TS bridge to the sidecar runner.
  modules/bio/
    pipeline/     ← Pipeline orchestrator (pure TS). Chains WASM + sidecar steps.

The WASM runtime is fully operational. Plugins are .wasm files that receive a JSON payload on stdin and write a JSON result to stdout.

// Add a plugin (file picker dialog).
await Liatir.plugins.add("qc.wasm");

// Call it.
const result = await Liatir.plugins.call("qc.wasm", {
  fn: "run",
  args: { input: "sample.fastq" },
}, /* timeoutMs */ 30_000);

Each call runs in an isolated job directory that is deleted after execution. Plugins have access to a persistent /storage directory across calls.

For native tools that cannot be compiled to WASM (e.g. samtools, minimap2).

To add a real sidecar:

1. Place the platform binary under src-tauri/binaries/ following Tauri's naming convention (<name>-<target-triple>).
2. Declare it in tauri.conf.json:

   "bundle": {
     "externalBin": ["binaries/samtools"]
   }

3. Add the shell:allow-execute permission for the binary in the capability file (src-tauri/permissions/liatir-bridge.toml).

Then call it from TS:

const result = await Liatir.sidecar.run("samtools", ["view", "-c", "sample.bam"]);

Chains WASM and sidecar steps in sequence. Stops at the first failure unless continueOnError is set.

const result = await Liatir.pipeline.run([
  {
    kind: "wasm",
    label: "QC",
    module: "qc.wasm",
    payload: { fn: "run", args: { input: "sample.fastq" } },
    timeoutMs: 60_000,
  },
  {
    kind: "sidecar",
    label: "Align",
    binary: "minimap2",
    args: ["-ax", "sr", "ref.fa", "sample.fastq"],
  },
]);

console.log(result.ok, result.steps.map(s => s.status));

Extension points (see src-ts/modules/bio/pipeline/_types.ts TODOs):

• Add bio pipeline presets as named functions (e.g. shortReadQC, alignShortReads)
• Add new step kinds (e.g. "http-fetch" for downloading reference genomes)
• Wire step output as input to the next step (currently each step is independent)

The sandboxed FS root is ~/.liatir/.main/ (data) and cache equivalent. WASM plugin storage lives at ~/.liatir/.main/_external_modules_storage/<plugin>/.

# Configure for local dev (writes window.env + tauri.conf.json)
bash scripts/local-dev-conf.sh

# Start Tauri dev
cargo tauri dev

• npm run liatir:publish -- --minor
• npm run liatir:publish -- --major
• npm run liatir:publish -- --patch
• npm run liatir:publish -- --bump minor
• npm run liatir:publish -- --version 1.10.0