Update installed apps#

Goal#

Refresh the locally cached container images (and, for local: registries, the on-disk app payloads) so installed apps match what’s published in the registry.

Minimal example#

from playmolecule import update_apps

update_apps()

Pulls newer versions of every image that’s already cached locally, and re-syncs any local registry’s acellera-protocols.zip if needed.

Pull every app, including ones you’ve never used#

By default update_apps() only updates images that are already in the local Docker / SIF cache. Pull everything published in the registry:

update_apps(pull_new=True)

Useful right after installing PlayMolecule on a new machine if you want all apps available offline.

Pick interactively#

update_apps(interactive=True)

Prints a numbered table of every available app with ✓ Installed / ✗ Not installed markers, then prompts:

Options:
  - Enter numbers separated by spaces to select specific apps (e.g., '1 3 5')
  - Enter 'all' to select all apps
  - Enter 'installed' to select only installed apps
  - Enter 'new' to select only non-installed apps
  - Press Enter to cancel

interactive=True implies pull_new=True.

Pass a service-account JSON (for local: registries)#

If your PM_REGISTRIES includes a local: URI backed by Acellera-provided GCS payloads, point at the service-account JSON Acellera issued you:

update_apps(service_acc_json="/etc/playmolecule/sa.json")

For pure docker:// registries the JSON is not needed — Docker handles auth via gcloud auth configure-docker.

Combine forms#

# Pull every app and reauth GCS with a service account in one call
update_apps(service_acc_json="/etc/playmolecule/sa.json", pull_new=True)

When to run it#

  • After Acellera notifies you of a new release.

  • After installing PlayMolecule on a new node and you want every app available without waiting for first-use pull.

  • As a recurring cron job on a shared install (paired with PM_REGISTRIES=local:/opt/playmolecule so every user benefits without each running update themselves).

Gotchas#

  • Updating an image may change its parameters or output names. Pin versions in scripts (see Select an app version) before running update_apps against a production install.

  • The function logs progress per image. For 30+ apps the output is long; redirect to a log file in cron use.

  • update_apps() does not delete obsolete images. Reclaim space with docker image prune (Docker) or by removing old *.sif files from PM_SIF_CACHE_DIR (Apptainer).

See also#