seqdesk

CLI launcher for installing and updating SeqDesk.

Usage

npm i -g seqdesk
seqdesk

Pass any installer flags directly:

seqdesk -y --dir /opt/seqdesk
seqdesk -y --use-pm2 --config ./infrastructure-setup.json
seqdesk -y --reconfigure --config ./infrastructure-setup.json
seqdesk -y --dir /opt/seqdesk --run-doctor

Check an installed directory:

seqdesk doctor --dir /opt/seqdesk
seqdesk doctor --dir /opt/seqdesk --url http://127.0.0.1:3000
seqdesk doctor --dir /opt/seqdesk --json

Apply hosted profile assets to an existing install:

seqdesk assets apply --dir /opt/seqdesk \
  --profile dev \
  --profile-code "$DEV_SETUP_CODE"

This reuses the installed app and applies profile-declared pipeline database assets and seed fixtures without reinstalling SeqDesk.

Run installed pipelines from the server shell:

seqdesk pipeline list --dir /opt/seqdesk --catalog all --enabled
seqdesk pipeline run metaxpath --dir /opt/seqdesk --study <study-id> --watch
seqdesk pipeline run fastq-checksum --dir /opt/seqdesk --order <order-id> --samples id1,id2 --json
seqdesk pipeline status <run-id> --dir /opt/seqdesk --watch
seqdesk pipeline logs <run-id> --dir /opt/seqdesk --type error --tail 200
seqdesk pipeline outputs <run-id> --dir /opt/seqdesk --json
seqdesk pipeline debug <run-id> --dir /opt/seqdesk --format text --out debug.txt
seqdesk pipeline cancel <run-id> --dir /opt/seqdesk

Pipeline commands run locally against the installed app database and use the same SeqDesk run records and launcher services as the web UI. They do not require browser login; shell access to --dir is treated as operator access. By default the first FACILITY_ADMIN user is used for attribution, or pass --user-email [email protected] when starting a run.

For a full manual test flow, see MANUAL_INSTALL.md.

Notes

• The npm launcher is the supported public install entry point.
• The launcher downloads https://seqdesk.com/install.sh over HTTPS and executes it with bash internally. Users normally do not need to call the shell installer directly.
• Publishing this npm package does not update the public curl installer. Changes to the shell installer become visible at https://seqdesk.com/install.sh only after the SeqDesk.com public/install.sh file is updated and deployed.
• By default it sets SEQDESK_VERSION to this package version (unless already set).
• The installer writes a timestamped log to /tmp/seqdesk-install-*.log unless SEQDESK_LOG is set.
• Interactive installs show a compact spinner for long-running work; command output stays in the install log.
• seqdesk doctor runs locally and does not download the installer. It checks install files, PostgreSQL reachability, runtime config, auth providers, and setup status when the app URL is known.
• seqdesk assets apply runs locally against an existing install. It resolves hosted install profiles into a temporary file, calls the installed scripts/apply-install-profile-assets.mjs script, and removes the temporary profile file after the command exits.
• seqdesk pipeline ... dispatches to the installed scripts/pipeline-cli.js script so CLI-started runs follow the same local server configuration, pipeline packages, execution policy, and compatibility guards as UI-started runs.
• Successful installs print a matching seqdesk doctor command. Pass --run-doctor to run it automatically when the CLI is available.

Publishing

The package version is auto-synced from the root package.json during publish (prepublishOnly), so you only bump the app version once.

cd npm/seqdesk
npm publish --access public