This repository contains a barebones framework for analyses and tutorials from the Asthma Collaboratory.
The initial directory structure is shown below. Feel free to adapt it to your needs.
├── LICENSE # defaults to GPL v3
├── README.md # a top-level README for developers using this project
├── DESCRIPTION # a package header for R (not useful otherwise)
├── .gitignore # all files that Git should _not_ commit
├── .travis.yaml # build configuration for TravisCI
├── run_analysis.sh # user-friendly button to push for running all analysis steps
├── env.sh # a template script for seeding environment variables; save as ".env"
│
├── analysis
│ ├── bin # any binaries (downloaded, softlinked, or otherwise) for the project
│ ├── data # all data necessary for project
│ ├── results # a folder for all analysis results
│ └── figures # generated graphics and figures to be used in reporting
│
├── docs # a place to store documentation (Sphinx, Jupyter notebooks, etc.)
│
├── src # all source code for the analysis, with 1 folder per step
│ ├── 01_step1
│ │ └── 01_run_step1.sh
│ ├── 02_step2
│ │ └── 01_run_step2.sh # notice that each substep of a step is ordered numerically starting from 1
│ ├── 03_step3
│ │ └── 01_run_step3.sh