Reference

Bash shell commands

Command line cheat sheet from Tower

pwd: print working directory

ls: list contents of directory

cd: change directory

mkdir: make directory

cat: send file or files to output (in most cases, print to shell)

head: output first parts of a file or files

tail: output last parts of a file or files

mv: rename or move a file or files. Syntax for renaming a file: mv FILENAME NEWFILENAME

cp: copy a file or files. Syntax: cp FILENAME NEWFILENAME

>: redirect output. Syntax with cat: cat FILENAME1 FILENAME2 > NEWFILENAME

rm: remove a file or files. USE WITH CAUTION!!!

Git commands

• GitHub git cheat sheet
• Git cheat sheet from Tower

git init: create a new local git repository

git status

view the status of your files in the working directory and staging area

git add

tell git to start tracking a file, or a series of files

git commit

save file changes from the staging area permanently to the project history

git push

upload all commits to a remote repository, such as GitHub

git log

show history of commits in reverse chronological order

git diff

show changes made to tracked files

git pull

download upstream changes and merge them into your local repository

git remote add origin

add a remote repository named ‘origin’, to upload changes to or download changes from

Markdown

• GitHub Guide to Mastering Markdown
• Markdown cheat-sheet for quick reference

Getting Started With Git

• An author at Webtuu.com provided both a clear introduction to git for absolute beginners and a follow-up git basics and branching blog post
• This recent Git guide for beginners covers the basics and includes tips for both Github and Gitlab
• For more in-depth coverage, Scott Chacon and Ben Straub’s “Pro Git” book is available as an online resource here

Hands-on Learning and Guides for Git

• The GitHub help pages are a good place to start
• GitHub has ‘activities’ which aim to explain how git works
• GitHub also has interactive tutorials for their online version (Learning Labs) and for using Git offline (Git-It)
• Atlassian has in depth and clear tutorials on using Git
• “Dang It, Git” provides a great quick walkthrough of how to fix common errors for Git beginners

Getting Started with Docker

• Docker Tutorial for Beginners in 1 hour by Mosh on Youtube
• Docker Tutorial for Beginners in 3 Hours on Youtube
• Carpentries lesson on Reproducible computational environments using containers will introduce Singularity which is a containerization solution tailored for scientific and HPC workloads
• Check out other Community Developed lessons on Carpentries