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Tooling status and version watch

Last reviewed: 2026-08-30

This page records public upstream versions, the baselines represented by this repository, and the level of public integration evidence. It is a knowledge base, not a live service-status page.

Status terms

  • Available: the tool is public and has a documented installation or access route.
  • Checked baseline: a public fixture and repeatable command have previously produced the expected output shape. This documentation review did not rerun those tools.
  • Adopted: repository contracts or runners consume that checked output shape.
  • Planned: the tool is relevant, but this repository does not yet make an integration claim.
  • Gated: access, licensing, redistribution, or resource requirements prevent a fully public integration.

A newer upstream release does not automatically replace a checked baseline. Promote a version only after a public fixture and output-contract check.

Version watch

Tool Current upstream Public baseline in this repo Status Note
antiSMASH 8.0.4 8.0.4 Checked baseline Bacterial and fungal BGC calling
plantiSMASH 2.0.4 2.0.4 Checked baseline Plant BGC calling; non-editable source installation
DeepBGC 0.1.31 0.1.31 Checked baseline ML-based BGC scoring
cblaster 1.4.2 >=1.4.0 Available Recheck the packaged minimum against 1.4.2 before promoting
clinker 0.0.32 >=0.0.32 Available HTML plot output uses --plot <path>
JCVI 1.6.6 >=1.6.5 Available MCScan synteny workflow
MMseqs2 18-8cc5c 18 Checked baseline Large protein search
Foldseek 10-941cd33 10 Checked baseline Structure search
MIBiG 4.0 4.0 Available Curated BGC reference data
igv-reports 1.16.3 >=1.16.2 Available Static genome review reports
Cytoscape.js 3.34.2 3.33.3 Checked baseline Recheck before updating the vendored/CDN baseline
Quarto 1.10.18 1.9.37 Checked baseline 1.11 is prerelease; recheck manuscript output before promoting
InterProScan 5.78-109.0 5.x Available Current release bundles Pfam 38.2
Pfam 38.2 37.x Available Update dependent database manifests together
Plant Metabolic Network 17.0 access by provider terms Gated Do not redistribute provider data
HIT-EC public repository none Planned Public source exists; no public fixture is committed here
ESM-C 6B provider/model terms none Gated Large-model access and compute requirements

Sources: antiSMASH releases, plantiSMASH releases, cblaster on PyPI, clinker, JCVI on PyPI, MMseqs2 releases, Foldseek releases, igv-reports on PyPI, Cytoscape.js, Quarto releases, InterProScan release notes, and PMN 17.

Adopted capability groups

The public contracts cover these capability groups:

  • source and accession scouting;
  • sequence and profile search;
  • BGC calling and comparison;
  • domain and function annotation;
  • structure search and representation;
  • synteny and genome-context review;
  • report and visualization generation.

An adopted group may have more tools in the inventory than packaged runners. The per-tool guides identify the subset with public quickstarts or wrappers.

Planned or gated integrations

  • cblaster + clinker: available upstream; the local-genome route needs GenBank inputs and a public end-to-end fixture.
  • CLEAN + HIT-EC: public sources are available; the combined output contract still needs a public fixture.
  • Large structure/model lanes: database size, model terms, and compute requirements must be recorded before adoption.
  • PMN data: access and redistribution remain governed by the provider’s current terms.

Maintenance rule

For each version change:

  1. link the upstream release source;
  2. run a public or synthetic fixture;
  3. record the command, version, output shape, and hash;
  4. update the relevant quickstart and wrapper;
  5. update the packaged documentation mirror;
  6. avoid claims that depend on private infrastructure or unpublished data.