Build Unity Application Package Generator

[mcduffie]

Make use of MAAP application-pack-generator for Unity

Planned steps for this build tool:

1. Push copy of Git repo into Gitlab
2. Build Docker image using repo2docker (Adapt app-pack-generator method, possibly modify and push pull request)
3. Push Docker image into registry (Adapt app-pack-generator method, possibly modify and push pull request)
4. Created CWL files from application metadata and Docker registry URL (app-pack-generator)
5. Push application package registry into Gitlab (possibly avoid and store CWL in Dockstore)
6. Use CWL files to register application into Dockstore

[mcduffie]

• Figured out how run app-pack-generator created CWL files
• Requires --no-read-only argument to cwltool
• Outstanding bug in app-pack-generator in regards to creating output directory
• Currently requires files from a notebook to be put into this directory, they decided to deprecate the stage-out feature
• Max Zhan is okay with Unity taking over development because their MAAP funding has run out
• I will take over modifying app-pack-generator into a Python library

[mcduffie]

• Fixed app-pack-generator to:
  • Create designated output directory
  • Pass output directory name to notebook instead of having it assume a path
• Now have a working end to end notebook example

[mcduffie]

Modified app-pack-generator to have the correct logic and call when a alternative config for repo2docker is supplied