On 17 March 2016 at 03:58, Kandauda Amila De Zoysa Karunathilaka <[email protected]> wrote:
> thank you for given instruction. > > I didn't have clear idea about following tasks. Can you give small > description about your requirement of this project. > What do you mean about JSON model for describing a docker run command?. Its > mean Do you want tanverna workflow docker image? or Do you want add docker > into tanverna? In Taverna 3, all activities in a workflow are configured using a small JSON object - the actual content and structure of that JSON depends on the activity type. A "docker run" command has many parameters: https://docs.docker.com/engine/reference/commandline/run/ https://docs.docker.com/engine/reference/run/ while some of them are not too relevant for execution of a tool from within Taverna (e.g. --dns), many of them are, e.g. --volume --publish --rm --env --name A new Taverna Docker Tool Activity wouldn't simply have a configuration { "command": "run --name mysql-surechembl --restart=always -v /media/SSD/stain/ims/surechembl-mysql:/var/lib/mysql -e MYSQL_ALLOW_EMPTY_PASSWORD=yes -e MYSQL_DATABASE=ims -e MYSQL_USER=ims -e MYSQL_PASSWORD=ims -d mysql" } As that you can already do with the Tool activity by adding "docker" to the command. So it could be more something like { "image": "mysql", "volumes": { "/media/SSD/stain/ims/surechembl-mysql": "/var/lib/mysql" }, "environment": { "MYSQL_ALLOW_EMPTY_PASSWORD": "yes" }, "detach": "true", "command": "mysql" } In that way it would be easier to generate/modify these programmatically, e.g. from a Taverna Docker UI binding for the Taverna Workbench. At execution time this could either be converted to the equivalent docker command, or (perhaps better) send it to the docker engine REST interface. https://docs.docker.com/engine/reference/api/docker_remote_api/ It is probably good to align with the docker-compose.yml syntax https://docs.docker.com/compose/overview/ Feel free to comment on https://issues.apache.org/jira/browse/TAVERNA-901 and the other Docker threads on this list. -- Stian Soiland-Reyes Apache Taverna (incubating), Apache Commons RDF (incubating) http://orcid.org/0000-0001-9842-9718
