NEON EDUCATION bio photo

NEON EDUCATION

Devoted to open data and open source in science and education.

View All Tutorials

Tags

R programming (56)
Hierarchical Data Formats (HDF5) (15)
Spatial Data & GIS (22)
LiDAR (10)
Raster Data (14)
Remote Sensing (25)
Data Visualization (4)
Hyperspectral Remote Sensing (18)
Time Series (17)
Phenology (8)
Vector Data (6)
Metadata (1)
Git & GitHub (7)
(1) (1) (14) (1) (1) (1) (1)

Tutorial by R Package

dplyr (9)
ggplot2 (18)
h5py (2)
lubridate (time series) (7)
maps (1)
maptools (1)
plyr (2)
raster (26)
rasterVis (raster time series) (3)
rgdal (GIS) (24)
rgeos (2)
rhdf5 (11)
sp (5)
scales (4)
gridExtra (4)
ggtheme (0)
grid (2)
reshape2 (3)
plotly (5)

View ALL Tutorial Series




Twitter Youtube Github


Blog.Roll

R Bloggers

Overview

Checklist

Once you have Git, Bash, R, and RStudio installed, you are ready to configure Git.

On this page you will:

  • Create a directory for all future GitHub repositories created on your computer

To ensure Git is properly installed and to create a working directory for GitHub, you will need to know a bit of shell. Please find a crash course below.

Crash Course in Shell

The Unix shell has been around longer than most of its users have been alive. It has survived so long because it’s a power tool that allows people to do complex things with just a few keystrokes. More importantly, it helps them combine existing programs in new ways and automate repetitive tasks so they aren’t typing the same things over and over again. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including “high-performance computing” supercomputers).

This section is an abbreviated form of Software Carpentry’s The Unix Shell for Novice’s workshop lesson series. Content and wording (including all the above) is heavily copied and credit is due to those creators (full author list).

Our goal with shell is to:

  • Set up the directory where we will store all of the GitHub repositories during the Institute,
  • Make sure Git is installed correctly, and
  • Gain comfort using bash so that we can use it to work with Git in Week 2.

Accessing Shell

How one accesses the shell depends on the operating system being used.

  • OS X: The bash program is called Terminal. You can search for it in Spotlight.
  • Windows: Git Bash came with your download of Git for Windows. Search Git Bash.
  • Linux: Default is usually bash, if not, type bash in the terminal.

Bash Commands

$ 

The dollar sign is a prompt, which shows us that the shell is waiting for input; your shell may use a different character as a prompt and may add information before the prompt.

When typing commands, either from these tutorials or from other sources, do not type the prompt ($), only the commands that follow it. In these tutorials, subsequent lines that follow a prompt and do not start with $ are the output of the command.

listing contents - ls

Next, let’s find out where we are by running a command called pwd – print working directory. At any moment, our current working directory is our current default directory. I.e., the directory that the computer assumes we want to run commands in unless we explicitly specify something else. Here, the computer’s response is /Users/neon, which is NEON’s home directory:

$ pwd

/Users/neon

Data Tip: Home Directory Variation - The home directory path will look different on different operating systems. On Linux it may look like /home/neon, and on Windows it will be similar to C:\Documents and Settings\neon or C:\Users\neon. (It may look slightly different for different versions of Windows.) In future examples, we’ve used Mac output as the default, Linux and Windows output may differ slightly, but should be generally similar.

If you are not, by default, in your home directory, you get there by typing:


$ cd ~

Now let’s learn the command that will let us see the contents of our own file system. We can see what’s in our home directory by running ls –listing.

$ ls

Applications   Documents   Library   Music   Public
Desktop        Downloads   Movies    Pictures

(Again, your results may be slightly different depending on your operating system and how you have customized your filesystem.)

ls prints the names of the files and directories in the current directory in alphabetical order, arranged neatly into columns.

Data Tip: What is a directory? That is a folder! Read this section on Directory & Folder if you find the wording confusing.

Change directory – cd

Now we want to move into our Documents directory where we will create a directory to host our GitHub repository (to be created in Week 2). The command to change locations is cd followed by a directory name if it is a sub-directory in our current working directory or a file path if not. cd stands for “change directory”, which is a bit misleading: the command doesn’t change the directory, it changes the shell’s idea of what directory we are in.

To move to the Documents directory, we can use the following series of commands to get there:

$ cd Documents

These commands will move us from our home directory into our Documents directory. cd doesn’t print anything, but if we run pwd after it, we can see that we are now in /Users/neon/Documents.

If we run ls now, it lists the contents of /Users/neon/Documents, because that’s where we now are:

$ pwd

/Users/neon/Documents
$ ls


data/  elements/  animals.txt  planets.txt  sunspot.txt

To use cd, you need to be familiar with paths, if not, read the section on Full, Base, and Relative Paths .

Make a directory – mkdir

Now we can create a new directory called GitHub that will contain our GitHub repositories when we create them later. We can use the command mkdir NAME– “make directory”

$ mkdir GitHub

There is not output.

Since GitHub is a relative path (i.e., doesn’t have a leading slash), the new directory is created in the current working directory:

$ ls

data/  elements/  GitHub/  animals.txt  planets.txt  sunspot.txt

Data Tip: This material is a much abbreviated form of the Software Carpentry Unix Shell for Novices workhop. Want a better understanding of shell? Check out the full series!

Is Git Installed Correctly?

All of the above commands are bash commands, not Git specific commands. We still need to check to make sure git installed correctly. One of the easiest ways is to check to see which version of git we have installed.

Git commands start with git. We can use git --version to see which version of Git is installed

$ git --version

git version 2.5.4 (Apple Git-61)

If you get a git version number, then Git is installed!

If you get an error, Git isn’t installed correctly. Reinstall and repeat.

Setup Git Global Configurations

Now that we know Git is correctly installed, we can get it set up to work with.

The text below is modified slightly from Software Carpentry’s Setting up Git lesson.

When we use Git on a new computer for the first time, we need to configure a few things. Below are a few examples of configurations we will set as we get started with Git:

  • our name and email address,
  • to colorize our output,
  • what our preferred text editor is,
  • and that we want to use these settings globally (i.e. for every project)

On a command line, Git commands are written as git verb, where verb is what we actually want to do.

Set up you own git with the folowing command, using your own information instead of NEON’s.

$ git config --global user.name "NEON Science"
$ git config --global user.email "neon@BattelleEcology.org"
$ git config --global color.ui "auto"

Then set up your favorite text editor following this table:

Editor Configuration command
nano $ git config --global core.editor "nano -w"
Text Wrangler $ git config --global core.editor "edit -w"
Sublime Text (Mac) $ git config --global core.editor "subl -n -w"
Sublime Text (Win, 32-bit install) $ git config --global core.editor "'c:/program files (x86)/sublime text 3/sublime_text.exe' -w"
Sublime Text (Win, 64-bit install) $ git config --global core.editor "'c:/program files/sublime text 3/sublime_text.exe' -w"
Notepad++ (Win) $ git config --global core.editor "'c:/program files (x86)/Notepad++/notepad++.exe' -multiInst -notabbar -nosession -noPlugin"
Kate (Linux) $ git config --global core.editor "kate"
Gedit (Linux) $ git config --global core.editor "gedit -s -w"
emacs $ git config --global core.editor "emacs"
vim $ git config --global core.editor "vim"

The four commands we just ran above only need to be run once: the flag --global tells Git to use the settings for every project in your user account on this computer.

You can check your settings at any time:

$ git config --list

You can change your configuration as many times as you want; just use the same commands to choose another editor or update your email address.

Now that Git is set up, you will be ready to start the Week 2 materials to learn about version control and how Git & GitHub work.

Data Tip: GitDesktop is a GUI (one of many) for using GitHub that is free and available for both Mac and Windows operating systems. In NEON Data Skills workshops & Data Institutes will only teach how to use Git through command line, and not support use of GitDesktop (or any other GUI), however, you are welcome to check it out and use it if you would like to.