Varvis Download CLI

Summary

The varvis-download package provides an independently developed free software command-line interface (CLI) for downloading BAM, BAI, and VCF files from the varvis® API. It supports authentication, session management, file filtering, proxy configuration, archived file restoration, genomic range downloads, and reporting for bioinformatics workflow automation.

Non-interactive / CI usage

For scripted or automated runs (CI pipelines, cron jobs, containers), avoid the interactive password prompt and archive-restoration prompt:

• Password: pass --password-stdin to read the password from the first line of stdin (mirrors docker login --password-stdin), or set the VARVIS_PASSWORD environment variable. Credentials resolve at CLI flag > environment variable > config file precedence — an explicit --username/--password/--target always wins over VARVIS_USER/VARVIS_PASSWORD/VARVIS_TARGET, which in turn win over the config file.
• Archive restoration: on a non-interactive run the default ask mode cannot prompt, so it is automatically downgraded to no — archived files are skipped (with a warning) and non-archived files still download. To restore archived files in automation, pass --restoreArchived force; to silence the warning, pass --restoreArchived no. Only an explicit --restoreArchived ask or --restoreArchived all fails fast on a non-TTY, since those deliberately request a prompt the environment cannot provide.

Example:

echo "$VARVIS_PASSWORD" | node varvis-download.cjs \
  --username "$VARVIS_USER" --password-stdin --target "$VARVIS_TARGET" \
  --analysisIds AN00001 --restoreArchived force

Intended Use

This software is provided solely for research, educational, development, interoperability, and bioinformatics workflow automation purposes. See the full Intended Use documentation for regulatory boundaries and user responsibilities.

License

This project is licensed under the GNU General Public License v3.0 (GPLv3). See the LICENSE file for details.

Documentation

The full documentation is available at laborberlin.github.io/varvis-download/.

It covers:

• Requirements and installation
• Configuration and environment variables
• CLI usage, filtering, archive handling, and range downloads
• API reference and development workflow
• Intended use and disclaimer

Disclaimer

The varvis® logo is a registered trademark of Limbus Medical Technologies GmbH and is used in this project with permission. This project is independent and is not affiliated with, endorsed by, or officially supported by Limbus Medical Technologies GmbH.