The proposed GSOC project is to add support for invoking Docker containers within Taverna by adding a Docker Activity plugin.
- Propose JSON model for describing a docker run command
- (Optional) Validate Docker activity config, e.g. can the docker image be pulled?
- Investigate: New Docker activity, or modify existing External Tool activity?
- Make/modify a Taverna Activity plugin for executing Docker (may or may not be based on the External Tool activity)
- (Optional) Capture docker metadata and add to workflow run provenance (e.g. which docker image ID was pulled)
- (Optional) Add Bioboxes support
- (Optional) Integrate with CWL support (TAVERNA-900)
Other Taverna/Docker--related tasks can of course also be proposed by the students.
Docker is a Linux container virtualization platform. A Linux container is a special kernel feature, which similar to chroot jails behave as a separate machine, but unlike Virtual Machines do not have the overhead of virtualization of hardware.
Docker is popular in the devops movement as it provides an easy way to install dependencies for software development and deployment, e.g. to run servers for mySQL, Apache Solr or node.js.
In brief a Docker Image contains a virtual Linux file system (e.g. a miniature Debian installation). A Docker Container is a particular execution of a Docker Image, which typically runs a single process as installed within the container, and may have network ports exposed to the world, or have parts of the host computer's file system mounted within the inner container.
One great advantage of Docker is that it simplifies tool installation, as each Docker image is a self-contained Linux distribution which don't have to be compatible with the host computer (beyond the kernel).
For Windows and OS X users Docker automatically manage a virtual machine running the Linux containers, but Docker containers can also be deployed on the cloud or a local cluster, e,g. using Docker Machine.
Docker images can be created from a Dockerfile, which basically lists the commands to run to prepare the image. Docker images can be chained together using base images - for instance to build on an image with mySQL, the Dockerfile says FROM mysql.
Thus Docker is also an important tool for reproducibility, as these images can be automatically kept up to date and are distributed through the Docker hub. In bioinformatics, this has led to Bioboxes, a standard for creating interchangable bioinformatics software containers.
Apache Taverna (incubating) is a Java-based workflow system with a graphical design interface. Taverna workflows can combine many different service types, including REST and WSDL services, command line tools, scripts (e.g. BeanShell, R) and custom plugins (e.g. BioMart).
Taverna workflows can be executed on the desktop, on the command line, or on a Taverna server installation, which can be controlled from a web portal, a mobile app, or integrated into third-party applications.
Taverna is used in a wide range of sciences for data analysis and processing, including bioinformatics, cheminformatics, biodiversity and musicology. Workflow engine features include provenance tracking, implicit parallelism/iterations, retry/failover and looping.
Taverna workflows are commonly shared on myExperiment, and can either be created graphically in the Taverna workbench, programmatically using the Taverna Language API or by generating workflow definitions in the SCUFL2 format.
Interested GSOC students are requested to engage early with the dev@taverna mailing list to describe their ideas for approaching this project, to clarify the tasks and for any questions and issues.
As a first step, the prospective applicant should leave a comment on this Jira issue to indicate their interest, and the GSOC mentors would be happy to assist on any questions.
As the project starts we are expecting the student to become part of the dev@taverna community to regularly discuss their progress.
An important part of GSOC is the personal mentoring from existing members of the open source community. Our job is not just to teach you how to successfully get through the GSOC programme, but also to motivate you and make sure you progress. We will show you how to contribute to open source, debug, improve, document, test and release your code as part of Apache Taverna.
The GSOC mentors for Apache Taverna have experience from guiding multiple earlier GSOC students and local students, and can be contacted privately for day-to-day interaction and trouble-shooting.
Mentors for this GSOC project:
- Stian Soiland-Reyes