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From "Deh-Jun Tzou (JIRA)" <j...@apache.org>
Subject [jira] [Issue Comment Deleted] (TAVERNA-900) GSOC: Add Common Workflow Language support to Taverna
Date Sat, 14 Apr 2018 20:39:00 GMT

     [ https://issues.apache.org/jira/browse/TAVERNA-900?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel

Deh-Jun Tzou updated TAVERNA-900:
    Comment: was deleted

(was: Hello!

My name is Deh-Jun Tzou and I'm currently a first year Master's student at UMass Amherst.
I have experience developing a workflow system using AWS services and have played with established
workflow engines such as Nextflow and Toil. I have also written workflows using CWL and have
run them using the reference implementation cwltool. I'm really interested in workflow engines
in general and feel that adding CWL support to Taverna is a great idea for improving portability.
Is there any part of the source code you can direct me to so that I can get a better idea
of how this support can be added?)

> GSOC: Add Common Workflow Language support to Taverna
> -----------------------------------------------------
>                 Key: TAVERNA-900
>                 URL: https://issues.apache.org/jira/browse/TAVERNA-900
>             Project: Apache Taverna
>          Issue Type: Story
>          Components: Taverna Language, Taverna Workbench Common Activities
>            Reporter: Stian Soiland-Reyes
>            Priority: Major
>              Labels: cwl, docker, gsoc2016, gsoc2018, java, json, json-ld, python, workflow,
> h2. GSOC: Add CWL support to Taverna
> The proposed GSOC task is to add support for  [Common Workflow Language|http://commonwl.org/]
 (CWL) in [Apache Taverna|http://taverna.incubator.apache.org/] (incubating). 
> The Apache Taverna community believe CWL support can be added to Taverna in a progressive
fashion, and therefore the GSOC student can achieve success in multiple ways - and depending
on her/his interests and existing skills can choose to pursue *one or two of these tasks*
in detail, and if time permits can "top up" by exploring some of the remaining tasks more
briefly as prototypes.
> See the underlying [Jira issues|https://issues.apache.org/jira/issues/?jql=project%20%3D%20TAVERNA%20AND%20labels%20%3D%20cwl]
for further ideas.
> * Save Taverna workflows as CWL (TAVERNA-881) - basically generate YAML by inspecting
workflows using the Taverna Language API and follow the [CWL specifications|https://w3id.org/cwl/].
> * Read CWL workflows (TAVERNA-877) - Add a plugin to [Taverna Language API|https://github.com/apache/incubator-taverna-language/]
to parse CWL's YAML
> * Execute CWL tool descriptions (TAVERNA-878) - modify Taverna's [Tool activity|https://github.com/apache/incubator-taverna-common-activities/tree/master/taverna-external-tool-activity]
> * -Browse and use CWL tool descriptions from the workbench (TAVERNA-880) - modify GUI
plugin to select from a collection or registry of tool descriptions-
> * -Create a Docker tool for executing Taverna activities (TAVERNA-879) - this allows
any Taverna steps to be used by other CWL engines-
> Other Taverna or CWL-related tasks can of course also be proposed by the students.
> h2. CWL
> The [Common Workflow Language|http://commonwl.org/] (CWL) is a pragmatic approach to
a standardized workflow language for executing  command line tools on the cloud and on local
> CWL is a *YAML*-based dataflow format, describing how command line tools can be wired
together in a pipeline. An example workflow: https://github.com/common-workflow-language/workflows/blob/master/workflows/FestivalDemo/filtercount.cwl.yaml
> CWL has a [vibrant community|https://gitter.im/common-workflow-language/common-workflow-language]
and multiple implementations, including _Rabix_, _Galaxy_ and a Python-based reference implementation
> h2. Taverna
> [Apache Taverna|http://taverna.incubator.apache.org/] (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|http://taverna.incubator.apache.org/introduction/taverna-in-use/]
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|http://www.myexperiment.org],
and can either be created graphically in the [Taverna workbench|http://taverna.incubator.apache.org/download/workbench/],
programmatically using the [Taverna Language API|http://taverna.incubator.apache.org/download/language/]
or by generating workflow definitions in the [SCUFL2|http://taverna.incubator.apache.org/documentation/scufl2/]
> h2. Community engagement
> Interested GSOC students are requested to engage early with the [dev@taverna|http://taverna.incubator.apache.org/community/lists#devtaverna]
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. 
> We are also hoping the student would engage with the [CWL community|http://common-workflow-language.github.io/#Community_and_Contributing]
- particularly for questions on interpreting the CWL specifications and possibly even improving
them. This engagement might include participating in development of the [CWL Java SDK|https://github.com/common-workflow-language/cwljava/]
- although for GSOC evaluation purposes we will concentrate on your direct contributions to
Apache Taverna.
> h2. Mentors
> 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
> Mentors for this GSOC project:
> * Stian Soiland-Reyes
> * -Alan Williams-

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