Visit iplantcollaborative.org (iPlant) and request an account.
- Click Register for iPlant and follow the instructions. If asked what you plan to do at iPlant, be sure to mention you're taking Dr. Loraine's Introduction to Bioinformatics Programming at UNC Charlotte.
Request access to iPlant Atmosphere.
- Log in to iPlant. Click Apps and Services. Request access to iPlant Atmosphere.
Launch and VM and log in using ssh
- Once you have your iPlant account, log in and launch a new Atmosphere instance, also called a VM (stands for "virtual machine.")
- Record the IP address of your VM. This is listed in the Atmosphere Dashboard in the column labeled Public DNS name.
- Log on to your VM using ssh. Type the IP address (e.g., 188.8.131.52) instead of IP:
If your local machine is a Windows computer, you'll need to install what is called an "ssh client" in order to log into your iPlant VM. A popular ssh client program many people use is called putty. To get a copy, visit: http://www.putty.org/.
If your local machine is a UNIX machine, use the export command to set an environment variable called VM and set it equal to your iPlant VM IP address. Then, when you log in, type ssh username@$VM. This would be easier than trying to remember your VM's IP address.
For example, you can add this line to your .bash_profile script, the script that executes every time you create a new shell:
This sets the variable VM to an address. Then, to log into your VM, you would type this:
Explore the system
- Once you've logged in, look around. Change to the root directory and list the directories you find there.
- Most of these directories appear on every Unix system. Use google to research the /etc, /var, and /bin directories.
Question: What kinds of files typically reside in the following directories?
Use sudo to rule your VM
As you know from your reading, UNIX systems are designed to support multiple users of varying levels of expertise. However, there is one user (the "root" user) who has total control over the system.
On many systems, the root user can't log into the system in the same way an ordinary user would. This is mainly a security precaution.
Typically, if you want to modify or even read files that are owned by "root", you have to use sudo.This just means that you execute commands "as root" with full access privileges. Also, if you create a file using sudo, the file will be "owned" by the root user.
Question: What happened?
Probably you got an error; the system told you something like "Permission denied."
If yes, this is because the system is configured to not allow ordinary users to list the contents of this directory.
However, your user id, because you created the VM in the first place, should be on the list of users who have "sudo" privileges. That is, you can run commands as "root" if you precede them with the "sudo" command, like so:
Question: What happens now?
Read the wikipedia sudo article and the manual entry for sudo BEFORE YOU DO ANYTHING ELSE WITH SUDO.
Question: What file lists users with sudo privileges?
Question: The first time you run a command using sudo, you have to enter your password. For a short time after that, you can run additional commands using sudo without having to enter your password. Why is that?
To turn in, print a copy and insert your answers.