"The same set of analyses applied to the same set of data should produce the same set of results." Easier said then done! This repository provides a reproducible workflow making using tools such as;
- Rmarkdown (for reproducible documents)
- Makefile (for workflow directives)
- Docker (for isolating the environment for the analysis to run in)
- DockerHub (image hosting) and GitHub for sharing code + results
- Quick start options
- Problem
- Reproducible documents using Rmarkdown (walkthrough)
- Workflow directives using Makefile (walkthrough)
- Isolated environment using Docker (walkthrough)
- Sharing analyses using DockerHub and GitHub (walkthrough)
- Bugs and feature requests
- Contributing
- Copyright and license
- install Docker: version used for this demo (version 19.03.0)
- install Git: version used for this demo (version 2.24.3)
$ git clone https://github.com/phillip-a-richmond/reproducible_analysis_demo.git
$ cd reproducible_analysis_demo
$ make build
$ make run
- Navigate to http://localhost:8787
- login using username: rstudio and password: 123
- open terminal in RStudio and type:
$ make all
Convert the following set of steps into reproducible workflow:
-
Get data (.sh)
-
Run analysis (.py)
-
Visual results (.r)
-
Write paper (manually make word document)
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Have a bug or a feature request? Please add your request here: https://github.com/phillip-a-richmond/reproducible_analysis_demo/issues.
Please feel free to make a pull request if you would like to modify anything.
Copyright 2021 Phillip Richmond Inc.
Code released under the MIT license.