End-to-end walkthroughs, generated from the
examples/ directory.
BioLedger supports running tools on HPC clusters through each engine's native
🚧 Work in progress — automatic CSV-to-ISA-Tab conversion is still under construction. The workflow below describes the intended behavior, not a tested one yet.
This walkthrough loads an ISA-Tab dataset, imports a simple custom tool, runs it in a session, and packages the result. You'll need an LLM API key set (see the main README) and Docker running.
How to author BioLedger tool specs manually — wrapping third-party tools, custom scripts, or existing workflow engine tools. These specs live in your local store and can be used in sessions, fan-out, and crystallization.
BioLedger can discover tools from external repositories — the Galaxy Tool Shed, nf-core modules, and Snakemake wrappers — and run them with their native workflow engines. No translation to BioLedger specs is required.
A practical end-to-end example using BioLedger's library integration — no need to bring your own tools or data. This walkthrough downloads a reference genome and paired-end sequencing reads from the public BioLedger libraries, imports bioinformatics tools from the ToolSpec library, and runs a complete variant-calling pipeline: indexing → alignment → sorting → variant calling.