Data manager

This is a source repository for docker image to download data for dictyBase data migration tasks. The docker container setup is based on radial topology.

Usage

Build

docker build --rm=true -t dictybase/data-manager .

Run

Command line

docker run --rm dictybase/data-manager app -h

NAME:
   downloader - Download obo ontology from bioportal and github

USAGE:
   downloader [global options] command [command options] [arguments...]

VERSION:
   1.0.0

COMMANDS:
   help, h	Shows a list of commands or help for one command
   
GLOBAL OPTIONS:
   --folder, -f '/data/ontology'				Download folder
   --bioportal, --bp '--bioportal option --bioportal option'	Name of bioportal ontologies
   --github, --gh '--github option --github option'		Name of github ontologies
   --api-key 							Bioportal api key
   --help, -h							show help
   --version, -v						print the version

By default, it expects an extra data container with a data volume set to /data folder. In that case, the ontologies will be saved in /data/ontology.

Example

docker run -v /data --name ontodata progrium/busybox
docker run --rm dictybase/data-manager --volumes from ontodata \
    --api-key d8535830jerekcei --bp so --bp eco