rstudio_git_github_hpc
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.6%) to scientific vocabulary
Last synced: 10 months ago
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JSON representation
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Repository
Basic Info
- Host: GitHub
- Owner: annakrystalli
- License: mit
- Language: R
- Default Branch: master
- Size: 6.3 MB
Statistics
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 1
- Releases: 0
Created over 8 years ago
· Last pushed over 8 years ago
Metadata Files
Readme
License
Citation
README.md
rstudiogitgithub_hpc
workshop outline
main aim
To enable researchers to run their work on the cluster more easily and efficiently
objectives
- understand portability issues, how they affect working with the cluster and best practice in project setup.
- understand the basics of version control, remote repositories and how they can be used for syncing on the cluster.
- appreciate that often what makes life easier on the cluster makes life easier locally too.
- practice using the combination of tools that make the workflow most efficient.
- git
- github
- rstudio
- sharc
RSTUDIO -> local
Projects
- portability
- version control (git)
- pathways
- naming and filesystem conventions
- managing dependencies (packrat)
Git
- clone
- pull
- push
Sharc
- file system
- data storage
- ideally within the project (data are also version controlled) but not always possible
- on sharc
- on smb
- on google drive
- unix for cluster basics
- the scheduler
- set up overview
- brief overview of requesting resources
- workflow basics
- cluster etiquette
- R script submission bash script
- load R and any external libraries
- install first package interactively
- if not using packrat, ensure your scripts include both
install.packagesand load (library) dependencies
- passing arguments to R scripts
- qsub
What's the best way to keep your work on the cluster in sync?
Github
- explain linking concepts
- workflow charts
Git on the cluster
- same principles
- authentication issues
General pitfalls of synching through github
- merge conflicts
- branching (eg working with a master and devel branch)
Owner
- Name: Anna Krystalli
- Login: annakrystalli
- Kind: user
- Location: Syros, Greece
- Company: @r-rse
- Website: https://www.r-rse.eu
- Twitter: annakrystalli
- Repositories: 240
- Profile: https://github.com/annakrystalli
Research Software Engineering Service in #rstats at @r-rse. Ex @RSE-Sheffield. Editor @ropensci. Core team member @reprohack. Available for hire! 🚀😎
Citation (CITATION)
How should others cite this work?
GitHub Events
Total
Last Year
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| annakrystalli | a****i@g****m | 7 |
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 1
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 5.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- annakrystalli (1)