---
tags: foss-fall-21
---

# FOSS Fall 2021 - Week 7, Thursday

----
## Topic: Interactive analyses

**FOSS Materials/Useful Links**

- [Instant Feedback (please complete before you leave class)](https://cyver.se/foss-feedback)
- [Course Homepage](https://learning.cyverse.org/projects/foss/en/latest/index.html)
- [Course Schedule](https://learning.cyverse.org/projects/foss/en/latest/schedule.html)
- [Today's content](https://learning.cyverse.org/projects/foss/en/latest/05_version_control.html)

## Links

- [Reproducible Research in Computational Science](https://www.science.org/doi/10.1126/science.1213847)
- [Ten Simple Rules for Reproducible Computational Research](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285)
- [Scientific progress despite irreproducibility: A seeming paradox
](https://www.pnas.org/content/115/11/2632)
- [Project Jupyter](https://jupyter.org/)
- [iCommands documentation](https://learning.cyverse.org/projects/data_store_guide/en/latest/step2.html)
- [VICE guide](https://learning.cyverse.org/projects/vice/en/latest/)
- [Jason's VICE Webinar](https://cyverse.org/VICEwebinar)
- [Create github access token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token)
- [Conda package manager](https://docs.conda.io/en/latest/)

----
## Discussion and notes

1. Reproducibility discussion.

3. Use case example: Building a Github to Jupyter workflow using CyVerse.

**Steps**

1. Clone a repository of Jupyter notebooks from GitHub
to a space on the CyVerse Data Store

- Demonstrate using mybinder.org
- Demonstrate using VICE
- Fork to a personal GH repository
- `git clone repository_url`
- We will try: https://github.com/genomics-education-alliance/leptin-mouse-rnaseq-docker
- `git clone https://github.com/JasonJWilliamsNY/leptin-mouse-rnaseq-docker.git`
- Be sure you use your own username for the clone if you would like to version control this repo ex. `git clone https://github.com/UserName/leptin-mouse-rnaseq-docker.git`
- `iinit # setup iCommands`
- `iput -rP # put copy of your cloned repo in the Data Store`
- `iput -rP leptin-mouse-rnaseq-docker .`
- Clone using webshell

2. Launch and edit notebooks using a VICE instance
- VICE jupyter data science app: https://de.cyverse.org/apps/de/07a2d5b2-76e2-11eb-be5f-008cfa5ae621/launch?saved-launch-id=60054c75-0e80-4169-8a9b-51cba04f756d
- Syncronize changes on Data Store to web shell instance
- `irsync -rv i:/iplant/home/YOURUSERNAME/leptin-mouse-rnaseq-docker leptin-mouse-rnaseq-docker`

3. Push notebooks back to your forked repository
- Create a GH access token - "https://github.com/settings/tokens/new # use "cyverse_vice for Note; 7 days experationScopes: repo, write:packages, admin:org, admin:public_key, admin:repo_hook"
- Configure git on the webshell instance
- Install Github CLI
- See: https://github.com/cli/cli#installation
- `conda install gh --channel conda-forge`
- Cash credentials
- See: https://docs.github.com/en/get-started/getting-started-with-git/caching-your-github-credentials-in-git
- `gh auth login`
- Push back to Github

---

## Breakout Discussion questions & notes

1. How do you define reproducible science?

After discussing on your own, review definitions: [Reproducibility vs. Replicability: A Brief History of a Confused Terminology](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778115/)

2. How do these definitions apply to your research/teaching?

### Homework Reminders

Homework link will be sent out by Friday!

----