Open bioinformatics tooling

Reproducible tools and flows.

TAFFISH turns versioned tool repositories, containerized runtimes, and shell-native flows into a lightweight package ecosystem for everyday computational biology.

Install TAFFISH Browse Hub Read the preprint

Static Hub GitHub-hosted index

Versioned Apps 0.1.0-r1 style releases

Containers Docker, Podman, Apptainer

What it is

A practical layer between shell scripts and heavy workflow systems.

A small workflow language

Compose command-line bioinformatics tools with structured parameters, flow dependencies, and reusable app metadata.

A local package manager

Use taf to update the cloud index, install apps, resolve flow dependencies, and run tools in the selected container backend.

A static Hub

App repositories publish releases; GitHub Actions builds images and refreshes a static JSON index consumed by local users.

Runtime and implementation

Built in Common Lisp, delivered with SBCL and LispWorks, and run through container backends.

Container backends

Choose the runtime that fits the machine.

TAFFISH apps are designed to run through Docker, Podman, or Apptainer, including HPC-oriented environments where Apptainer is the natural choice.

Docker

Podman

Apptainer

Implementation

The core tooling stays close to the language.

The compiler, CLI, metadata handling, and index tooling stay in Common Lisp, with SBCL for open development and LispWorks solving Linux delivery.

Common Lisp

SBCL

LispWorks

Target environments

Unix-like shells first, with WSL as the Windows path.

TAFFISH is shaped around shell-native bioinformatics work on Linux and macOS; Windows users can use WSL2 with a configured container backend.

Architecture and distribution support may vary by TAFFISH release and app image; package metadata should declare amd64/arm64 availability when relevant.

Linux

macOS

Windows + WSL2

Get started

Install once, then let the index do the finding.

The canonical installers and backend notes live in the core repository. After taf is available locally, the first workflow is intentionally small.

Open installation guide

$taf update
$taf install <app>
$taf info <app>
$taf list --online

Hub architecture

GitHub repositories become installable TAFFISH apps.

1

Create an app repository

A root taffish.toml declares package metadata, command name, kind, source path, container hints, and optional upstream information.
2

Tag versioned releases

Release tags use the v0.1.0-r1 pattern, keeping upstream app versions and TAFFISH rebuilds distinguishable.
3

Build containers in Actions

Each app repository owns its own Dockerfile-based image build and publishes the image through GitHub infrastructure.
4

Refresh the static index

taffish-index scans app repositories, validates metadata, records dependencies and platform constraints, then writes JSON for taf.