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First-time setup wizard

The first time you open Yeliztli, a six-step wizard walks you through configuration and gets your data ready to analyse.

Step 1 — Disclaimer

Read and accept the disclaimer: Yeliztli is for educational and research use only and is not a diagnostic tool. (The full statement is on the Intended use & disclaimers page.)

Step 2 — Import from backup (optional)

If you have a previous Yeliztli backup (a .tar.gz archive), restore it here to bring back your samples, configuration, and any standalone reference files included in that archive. Reference-resident datasets can be downloaded again later. Skip this for a fresh install. See backup & restore.

Step 3 — Storage path

Choose where Yeliztli stores everything. The default is ~/.yeliztli/. The wizard shows available disk space and warns when it is low (a warning under ~80 GB; setup is blocked under ~60 GB). The larger threshold accounts for dbNSFP's transient source archive during setup; see system requirements for the breakdown.

Step 4 — External services

Both are optional and Yeliztli works without them:

  • PubMed contact email (recommended) — NCBI's terms of service ask for a contact email for literature lookups; providing one enables PubMed citation fetching for findings.
  • OMIM API key (optional) — enriches gene–disease associations. Request a key at omim.org/api.

These lookups use public identifiers only — never your genotypes (see Privacy).

Step 5 — Download reference databases

Yeliztli downloads the reference data needed to annotate your variants. Downloads stream with live progress and are resumable — if one is interrupted, a Resume button picks up from the saved partial instead of restarting. A database is only treated as installed once it is present and passes an integrity check, so a half-finished or corrupted download is reported honestly rather than failing silently during annotation. You can inspect and repair any database later under Settings → System Health → Database Health.

The required setup gate is ClinVar, gnomAD, dbNSFP, CPIC, GWAS Catalog, dbSNP, and MONDO/HPO. Setup cannot complete, and the dashboard is not reachable, until all seven are Ready. Most optional sources can be added later from Settings → Database Management; manual or bring-your-own sources use their documented local ingest path.

Plan for full first-run setup to take on the order of an hour or more. The exact time depends on bandwidth, CPU, disk speed, and which optional databases you choose. The largest required source is dbNSFP: after its large archive finishes downloading, Yeliztli still has to parse, build, and index the SQLite database. That CPU/disk-bound phase can run for a long time without a moving byte-progress bar; a database state of Downloading or Building in Settings → System Health → Database Health means the setup is still working. A Failed state on any required database blocks setup like low disk space; resume, clean, or retry that database before continuing.

For the full list of what is downloaded, sizes, sources, and licenses, see reference data.

Step 6 — Upload your data

Upload your raw genotype file. Yeliztli supports 23andMe (v3/v4/v5) and AncestryDNA (v2.0) exports as a .txt or as a single-file .zip containing the raw .txt; it auto-detects the vendor and format. Both services download your raw data inside a .zip by default, and Yeliztli accepts that archive when it contains exactly one raw .txt. Once parsing finishes, annotation runs automatically in the background, followed by the analysis modules.

Multiple files for one person

If you have tested with more than one service, you can add additional files later from the Upload page. Files from the same person — for example a 23andMe and an AncestryDNA export — can be grouped under one individual and optionally combined into a single merged sample.