Day 2: Software Carpentry

MATERIALS TOP

Install software

• Install the required software

Presentation

• Software carpentry and reproducible data analysis by Shaun Mahony

Software Carpentry

The basics of computational reproducibility: version control, documentation, automation

Instructor: Dr. Shaun Mahony

LESSONS TOP

Best Practices for Scientific Computing

• Best Practices in Scientific Research
• Best Practices for Scientific Computing, PLoS Biology, Jan. 2014

Shell scripting

• Shell scripting basics
• Running scripts on a cluster (ICS-ACI)
  • ICS-ACI onboarding slides
  • ICS-ACI reference sheet

Markdown

• 15 minute Markdown tutorial
• Original Markdown and CommonMark

Git

• Version control with git

GOING FURTHER TOP

Advanced Bash scripting

• Advanced Bash-Scripting Guide

Make

• Automation with make
• Snakemake: a different kind of automation

Alternatives to Git/GitHub

• Bitbucket: a different type of "GitHub"
• Fossil: a different type of source code managment

Alternatives to Markdown

• Asciidoc and Asciidoctor: a different type of text markup