CLI Cheat Sheet
All commands are subcommands of the helix console entry point. The most common flags mirror the Python API arguments.
CLI Session Contract
Helix’s CLI session behavior is governed by a versioned, executable black-box contract (currently v2).
CI validates it on Linux and macOS on PRs and pushes to main/master (path-filtered).
Artifacts emitted by this lifecycle include deterministic provenance fingerprints when HELIX_DETERMINISTIC=1.
Details: Helix CLI Session Contract v2.
| Command | What it does |
|---|---|
helix dna --input path.fna | GC stats + k-mer clusters |
helix triage --input path.fna --json triage.json | Combined GC/k-mer/ORF report (JSON + optional plots) |
helix spectrum --peptide NQEL --spectrum "…" | Theoretical spectra + leaderboard scoring |
helix rna mfe --fasta seq.fna --dotbracket out.dbn | Zuker-style MFE folding |
helix rna ensemble --fasta seq.fna --gamma 1.0 | Partition function + MEA/centroid + dot-plot/entropy |
helix protein --input protein.faa | Protein summaries/hydropathy (requires Biopython) |
helix viz triage --json triage.json --output triage.png | Plot triage payloads (requires matplotlib) |
helix viz hydropathy --input src/helix/datasets/protein/demo_protein.faa --window 11 | Plot hydropathy profile (Biopython + matplotlib) |
helix string search --pattern GATTACA --k 1 seqs.fna | FM-index exact search (k=0) or ≤k Myers hits with JSON output |
helix seed index --method minimizer --k 15 --window 10 seq.fna | Emit minimizers/syncmers + optional density plots |
helix seed map --ref ref.fna --reads reads.fna --k 15 --window 10 | Toy seed-and-extend mapping summary |
helix dbg build --reads reads.fna --k 31 --graph dbg.json | Build a DBG + optional GraphML |
helix dbg clean --graph dbg.json --out dbg_clean.json | Remove tips/bubbles via CLI |
helix dbg color --reads sample1.fna sample2.fna --k 31 | Produce colored DBG presence JSON |
helix motif find --fasta seqs.fna --width 8 --solver steme | PWM discovery via EM/STEME/online + optional JSON/plot |
helix sketch build --method minhash --fasta seq.fna --k 21 --size 1000 | Build a MinHash or HLL sketch |
helix sketch compare --method hll --fasta-a a.fna --fasta-b b.fna | HLL Jaccard/cardinality or Mash distance |
helix workflows --config workflows/plasmid_screen.yaml | Run YAML-defined pipelines |
helix partner run --outdir out --with-support-bundle --json-out out/partner_run.json | Design partner demo + support bundle (three seeded runs) |
helix validate pack ampseq_indel_profile_v1 --outdir out/validation --ci | Run a shipped validation pack and emit a verdict artifact |
helix verify verdict out/validation/ampseq_indel_profile_v1/verdict.json | Verify a signed validation verdict |
helix verify bundle helix-reference-validation-bundle-v1.2.3-linux.tar.gz --json-out verify_bundle.json | Verify a bundle of signed verdicts (+ machine summary JSON) |
helix replay path/to/session.helix.json --out out/ | Deterministically replay a session into artifacts + a canonical replay_receipt.v1.json |
helix artifacts build --config cfg.json --outdir out/bundle --sign --signing-key signer.ed25519 | Build and sign an artifact bundle (governance license required) |
helix verify out/bundle.zip | Verify a signed artifact bundle (offline; no local license needed) |
helix verify --kind repro repro_out | Verify CPU/GPU parity for repro bundle outputs |
Tip: add PYTHONPATH=src when running from the repo root or install with pip install -e ..
60-second trust demo (release receipts)
Replace <TAG> with a release tag (example: v1.2.3):
python -m pip install -U helix-governance && gh release download <TAG> --repo omniscoder/Helix --pattern "helix-reference-validation-bundle-<TAG>-linux.tar.gz" && gh release download <TAG> --repo omniscoder/Helix --pattern "helix-reference-validation-publisher-<TAG>-linux.pub" && helix verify bundle "helix-reference-validation-bundle-<TAG>-linux.tar.gz" --pubkey "helix-reference-validation-publisher-<TAG>-linux.pub" --json-out verify_bundle.json