# Deliverables - Cavatica 1

## Team Mango

- Ashley
- Chola
- Elmira
- Will

---

## Github
https://github.com/TeamMango/cavatica

## Accomplishments
* Reproduced [Cavatica network analysis](https://github.com/incertae-sedis/cavatica) in Jetstream (excluding Mango graph studio)
* Installed dependencies (e.g., R packages)
* Created singularity image
* Includes metadata (e.g., author, title, doi, last_update)
* Available on [SingularityHub](https://www.singularity-hub.org/collections/1322)
* Created a docker image
* Includes metadata (e.g., author, title, doi, last_update)
* Available on [DockerHub](https://hub.docker.com/r/griffinac/cavatica/~/dockerfile/)
* Ensured script. sh scripts conform to [Google Code Stylesheets](https://google.github.io/styleguide/Rguide.xml)
* Manual validation
* Created a Workflow [diagram](https://www.draw.io/?lightbox=1&highlight=0000ff&edit=_blank&layers=1&nav=1&title=Workflow#R7Zpdb5swFIZ%2FTaTtjkDK0ss1TT%2BkVpuaTbt24ABuDScyJh%2F79TuAnUBDVrqpJSrJRWS%2FtrF9jp8ArzJwJvH6WrJFdI8%2BiIFt%2BeuBczmw7fORS9%2B5sCkFd3heCqHkfikNd8KM%2FwYtWlrNuA9praNCFIov6qKHSQKeqmlMSlzVuwUo6rMuWAh7wsxjYl%2F9xX0Vler4zNrpN8DDyMw8tHTLnHlPocQs0fMNbCcoPmVzzMy1dP80Yj6uKpIzHTgTiajKUryegMhDa8JWjrs60Lpdt4REtRrglCOWTGRgllwsTG1MMMCn2OgqShVhiAkT0516UWwY8ktaVItULKg4pOIjKLXR6WWZQpJ2V7hDXOh%2BARdiggJlMaPjMxgHHumpkvgElRbXG8M8yEdgovSFhyOq729cxyLFTHomreYsMRmC6aY3nO%2ByMlCH6xowBiU31EGCYIov6yeE6YMWbvvtgk0FHe%2Bi%2BjMF%2BW3%2BmB9X2xJsDqIc%2BgALiX5Ga6TzzJY0h8eo%2BOnmx%2F3dZ71eCfBQnInK1NsUVter01vJ3iriCmYLVsRgRbTWM8QEDxMqexQ3oCBf5HNdES88CXUXgkwxnuStRV2Cl8mUIvEAaZkB621TuASpYP3X5OhWg9WmXl3tGB4aLarw61qvziZVKwk9ANdZr%2BCyG%2BAadQzXFV%2BTcAkLoBgmXj7VbZpmdG9pAZZ9AmsL1pGR9aVXZI0ayHI7Jmsigan8nnWJ3hMdYUpOnD9VteBqdOLKcDU6Mq7Oe8WV28DV%2BFi4mtGBzgSTXG1eA5d7gsvA5R4XXNsN9AOu8T5cJtidwfXV90m4Z0mIhaVQvX3dtiVsfCLsEGFDt2PEemVnmMDWEOvazmhArH4na8tZxQ%2FrPWfPHxM756xXzobZXI2zrp0NzRko5jPF9u5mLPGbyWvjfNgn5%2BOg89E5er2yPuwG68Pu2vqYJmkmC7sekwBlXNK14nQcbOsaMRR54wT94jXOiyBuR93JFzlk5HcO3XH4Io3n%2FmWGGmwOe9wc%2FrdC5jumquFly%2BJJVb3J5m04OVkchzhxrG45cY7D4vhHThocC8dqDv8bc9L4xlTCUm9qSczHsiz28GhIbevnuXdG5kXbN3%2BUn0W0HTYvHiO2nW992iEPeP5L%2BWLGnY%2F18vxfGX%2F%2B8vzOGSdp93%2BeonvlP1PO9A8%3D)

## Opportunities
* Add Mango to singularity image
* Add Mango to docker image
* Add citation network functionality
* Convert the tool to a R package
* Convert the tool to a web tool
* Determine if the sentence is in the methods section
* Run code on another set of software or methods
* Figure out WebGL to visualize the 3D graph and post on a website (or in Shiny)
* Create a workflow manager with [Makeflow](http://ccl.cse.nd.edu/software/makeflow/)
* Ensure all scripts conform to [Google Code Stylesheets](https://google.github.io/styleguide/Rguide.xml)
* Use Binder to have a one-click way to repeat the main workflow

## Lessons Learned
* Difficult to get all dependencies in one container
* GUI's are difficult for containers
* Easier to make code reproducible when you publish it.
* Importance of federation (Github, Slack), virtualization (Jetstream), and automation (Singularity) for reproducibility
* Kanban-style board on Github was useful for managing tasks
* Running a VM (Jetstream) was useful for building and testing because the OS, libraries, and programs are the same

## Reproducing Hydroshare 1

https://hackmd.io/3L-n-FD8QP6xrd4Iso0WtA