outpack.orderly

A temporary package to play around with outpack migration etc.

Installation

To install outpack.orderly:

remotes::install_github("mrc-ide/outpack.orderly", upgrade = FALSE)

Usage from docker

Usage:
  mrcide/outpack.orderly <src> <dest> [--once] [--minutes=<x>] [--custom=<cron-schedule>]

Options:
  --once                      Perform migration once.
  --minutes=<x>               Schedule migration every x minutes.
  --custom=<cron-schedule>    Schedule migration using cron.

You will have to first mount the orderly and outpack directories as volumes. orderly can be readonly.

docker run -v orderly:/orderly:ro \
           -v outpack:/outpack \
           mrcide/outpack.orderly /orderly /outpack --once

If running on a schedule, you most likely want to run in detached mode:

docker run -v orderly:/orderly:ro \
           -v outpack:/outpack \
           -d \
           mrcide/outpack.orderly /orderly /outpack --custom="* * * * *"

If not using named volumes, you probably want to run as the host user to avoid root owned files being created:

docker run -v /some/path/orderly:/orderly:ro \
           -v /another/path/outpack:/outpack \
           -d \
           -u $UID \
           mrcide/outpack.orderly /orderly /outpack --custom="* * * * *"

Usage without docker

Recommended usage is from docker but to run a one-off migration on metal, first install this package from source and then use ./orderly2outpack.R:

Usage:
  ./orderly2outpack.R <src> <dest>

License

MIT © Imperial College of Science, Technology and Medicine