HackMD
Deliverables - Cavatica 1
Team Mango
- Ashley
- Chola
- Elmira
- Will
Github
https://github.com/TeamMango/cavatica
Accomplishments
- Reproduced Cavatica network analysis 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
- Created a docker image
- Includes metadata (e.g., author, title, doi, last_update)
- Available on DockerHub
- Ensured script. sh scripts conform to Google Code Stylesheets
- Manual validation
- Created a Workflow diagram
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
- Ensure all scripts conform to Google Code Stylesheets
- 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
