Arvados

tom (on irc):

2:02 https://github.com/ga4gh/tool-registry-schemas
2:02 http://editor.swagger.io/#/?import=https://raw.githubusercontent.com/ga4gh/tool-registry-schemas/develop/src/main/resources/swagger/ga4gh-tool-discovery.yaml
2:02 https://www.dockstore.org:8443/api/v1/tools
2:02 curl https://www.dockstore.org:8443/api/v1/tools | jq .

Implementation:

• Add a “Run a tool” button in the panel header next to “Run a pipeline” in dashboard.

• Add a config parameter to workbench to configure the tool registry end-point

• When this button is pressed, present a “Choose a tool to run” modal similar to “Choose a pipeline to run” to the user
  • Get the tool json from the configured end point (do we want to cache this and pull at regular intervals or for each click?)
  • Present each version of each tool from the json as a separate link in the popup
    

    pcawg-merge-annotate - master
    pcawg-merge-annotate - 1.0.0
    …
    

  • When a link from the popup is clicked on, show the tool detail in preview pane on the right
  • When OK button is selected, create a CR with the selection as mount(s) and take the user to the CR page
  • The CR created for the selected tool version will have:
    • Name = tool - version (ex: pcawg-merge-annotate - master)
    • use mount kind json to store the selection
    • store the entire selected tool record including all version as mount point “/var/lib/cwl/tool”
    • store the selected tool version as mount “/var/lib/cwl/tool_version”

Out of scope for this story:

• Support for json mount kind

• Presenting appropriate input selection options based on the selected tool description

• Running the selected tool