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Installation
These are notes on installation for the various tools and packages we'll use throughout the course.
Before you arrive, you should install three things: a command-line terminal, R, and RStudio.
If you are bringing a Mac or Linux computer to work on, this is already taken care of for you. If you are bringing a Windows computer, you will need to set up a working command-line environment.
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If your operating system is Windows 10 or later, the operating system includes a way to run a command-line environment. You can follow the helpful steps outlined here to get set up.
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If you have an older Windows operating system, you can set up a command-line working environment relatively easily through Git for Windows by following these steps.
- Download the "Git-2.18.0-32-bit.exe" file from the Git for Windows download page
- After it is finished downloading, run the installer by opening the file and proceed through the installation:
- installing in the default folder location is fine
- for "Which components should be installed?", make sure the following boxes are checked: "On the Desktop"; "Git Bash Here"; "Git GUI Here"; "Associate .git* configuration files with the default text editor"; and "Associate .sh files to be run with Bash"
- the shortcuts default location is fine
- change the default Git editor to "Nano"
- on the "Adjusting your PATH environment" screen, select "Use Git from Git Bash only"
- just click "Next" on the remaining configuration windows, and "Install" at the final one
- When the installation is finished, you should be able to open a terminal window by launching Git Bash from your desktop.
R is a programming language that is extremely useful for statistical analysis and generating figures. Follow the instructions at the following pages to download and install the appropriate version for your operating system:
Mac – https://cran.r-project.org/bin/macosx/ (download the latest release "R-3.5.1.pkg")
Windows – https://cran.r-project.org/bin/windows/base/
Linux – https://cran.r-project.org/bin/linux/
Rstudio is an interface for R that not only makes everything you will do in R easier and more organized, but it’s also invaluable for reproducibility of your analyses as it makes it second-nature to generate and save log files (R scripts) of everything you’re doing.
Download and install the appropriate version of RStudio for your system from here: https://www.rstudio.com/products/rstudio/download/#download
There is an MBL-GUEST network that should work just fine. If you want to try connecting to the MBL-REGISTERED network, the username and password are both the same, and that is your first and last initials, followed by the numbers written next to the barcode on your MBL ID (the hard card you got from security after check-in).
If you are on the MBL-GUEST or eduroam WiFi network, start with Step 1, and then go to Step 2. If you are on the MBL-REGISTERED WiFi network, skip Step 1 and start at Step 2.
On your badge (name-tag badge with the pin), you have a username and password. That will be your account for the course.
To connect, we'll use ssh, a command that let's us establish a secure connection.
Step 1
At the command line type the following, but replace "<USERNAME>" with your username:
ssh <USERNAME>@class.mbl.edu
Don't include the brackets. For example, if your username were "bsmith", the command would look like ssh [email protected].
The first time you log in you will get a message about security. Type "yes", and press enter.
Then it will ask you for your password. Type the password listed on your badge and press enter; the cursor will not respond, but it is still being entered as you type.
Pro tip
If you have a crazy password, you can type it somewhere you can read it. Then copy and paste it.
So far, we just logged into what is called a 'gateway'. We won't be doing our work here though, we're going to take one more step and log into specific servers so we don't overload the computing resources.
Step 2
On your badge you also have something that says a class and a number, e.g. "class-09". That specifies which server you should be working on. So now we want to ssh into that specific server. so enter the following, again change the "<USERNAME>" to your username, and change the "<??>" to your specific class number:
ssh <USERNAME>@class-<??>
Again, don't include the brackets. For example, if our user bsmith had "class-09" as their class number, the command would look like: ssh bsmith@class-09.
Then if it asks for you password again, enter it the same way as above and press enter.
Now you're logged into the server that you'll use for much of the course.