Install and select database profiles

Run the interactive installer to view both profiles, their versions, and their download sizes:

pixi run setup

Select a profile by number or name. If config/local.config contains a previous selection, the prompt labels it as the default; press Enter to keep it. Bare pixi run ssuextract and pixi run example commands use this saved profile.

Install the curated profile

pixi run setup --database_profile curated

Install the IMG profile

pixi run setup --database_profile img

The installer downloads the archive listed in config/database_catalog.json, checks Zenodo for the latest database release, and verifies the release and archive checksums before installation. The bundled catalog is used if Zenodo cannot be reached during a first installation.

The terminal progress bar updates in place and fits the detected terminal width. Non-interactive logs report the start, completion, and intermediate progress every 10 seconds.

Setup stops after five consecutive transient download failures. If the retained bytes fail verification or the server rejects their byte range, setup makes one clean restart for that condition. Run the same setup command again after a stopped transfer. The next run requests the remaining bytes and verifies the complete archive size and SHA-256 digest before extracting it.

Update an installed profile

Pipeline runs print the installed database version and check Zenodo for the latest release. An interactive run asks before starting Nextflow when an update is available:

Database update available for img: v1.0.1 -> v1.0.2.
Update database now? [y/N]:

Enter y to download, validate, and install the release. Any other response keeps the installed profile for that run. Non-interactive runs print the update command and continue with the installed profile.

If the update fails, the installed profile remains in place and Nextflow does not start. Rerun the command to resume the download or repeat the release check.

Install the suggested update:

pixi run setup --database_profile curated --update

Interactive pixi run setup without --update uses the same confirmation prompt.

The existing profile remains in place until the downloaded archive and its contents pass validation.

Select a profile for one run

pixi run ssuextract --query data/my_dataset --outdir results/my_dataset-img --database_profile img

This option applies to one run and does not change the profile saved by setup.

Use another database root

pixi run ssuextract --database_path /path/to/ssuextract-databases --database_profile curated

The root must contain the selected profile directory and its manifest.json. Pipeline runs with an explicit --database_path report available releases but do not offer to replace the custom database root. Use pixi run setup with the same path and --update to replace it. The terminal prints this complete setup command when an update is available.

See database profiles for the installed files and taxonomy sources.