Rbbt is a reproducible workflow + data framework for scientific computing and bioinformatics.
- Run workflows locally or against remote workflow servers
- Work with large datasets using streaming TSV primitives
- Bootstrap software/data via Resources (with caching + provenance)
- Build workflows in Ruby, and (in modern Scout-based installs) implement workflow tasks in Python
- Integrate with LLM agents: workflow tasks as tools (and MCP tool support)
Pick your path (3 golden paths)
Run something now (quickstart) {: .btn .btn-primary } Install & setup {: .btn } Write workflows in Python {: .btn } Use workflows as LLM tools {: .btn }
1) I just want to run something → start with remote execution and a minimal CLI setup:
2) I want to develop workflows, but I don’t want to write Ruby → write task logic in Python and keep Ruby as orchestration:
3) I want to understand the framework / build an app → learn the core concepts (Workflow, TSV, Resources, HPC/remote):
In a hurry? (container quickstart)
If you just want a working rbbt CLI without a Ruby install, you can use the published container image:
wget "https://b2drop.bsc.es/index.php/s/ay9mqyD8CTE3GgA/download" -O ~/rbbt.singularity.img
alias rbbt='singularity exec -e ~/rbbt.singularity.img rbbt'
# sanity check
rbbt --help
(If your system uses Apptainer, replace singularity with apptainer.)
Rbbt and Scout (what’s the relationship?)
Historically, Rbbt started as the “Ruby Bioinformatics Toolkit”. The modern core has been split into smaller, reusable packages under the Scout ecosystem.
If you’re new: you can think of it as:
- Rbbt = the user-facing framework + ecosystem
- Scout = the core libraries that power modern Rbbt
Details and a repo map:
Example: run a workflow task remotely
One easy way to try Rbbt workflows is to use a remote workflow server (no local bootstrapping):
# list tasks and get help
rbbt workflow task https://rbbt.bsc.es/Sequence -h
rbbt workflow task https://rbbt.bsc.es/Sequence -h mutated_isoforms_fast
# translate gene symbols
rbbt workflow task https://rbbt.bsc.es/Translation tsv_translate -g TP53,MDM2,RB1
What’s in this documentation site?
- Start here (new, guided):
- Reference (new, concise):
- AI (new, Scout-AI overview):
- Legacy tutorials (existing content; being reorganized):