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.
Build
docker build --rm=true -t dictybase/data-manager .
Run
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.
docker run -v /data --name ontodata progrium/busybox
docker run --rm dictybase/data-manager --volumes from ontodata \
--api-key d8535830jerekcei --bp so --bp eco