Most Next Generation Sequencing (NGS) analysis is done via the command line with typed text commands rather than using Graphical User Interfaces (GUIs) that are more common in day to day computer use. Additionally, rather than analysis being confined to your personal computer/laptop it is often beneficial to access shared computer resources such as those at TACC. This is done via Secure Shell (SSH) programs. MacOS comes with a program called "terminal" which is where you will enter all the commands.

Tutorial Objectives:

  1. Launch Terminal from MacOS.
  2. Use ssh command to log into stampede2 on TACC.

Launching Terminal :

Use one of the following:

  1. Using the spotlight (shortcut command + spacebar) type 'terminal' and double click the icon.
  2. Open the finder and click on "Applications" on the left then navigate to: Utilities → Terminal

After which a window will open that looks like this:

*It is expected that "Daniels-MBP:~ ded" be replaced with something that makes sense to you, but will end with a "$" symbol.

Use ssh command to log into stampede2:

You will need 4 pieces of information to log into stampede2:

  1. Your TACC userID

    1. If you do not have a TACC ID sign up for one here.

  2. Hostname of the remote computer you are trying to log into

    1. For this class the hostname will be "stampede2.tacc.utexas.edu" for stampede2.

  3. Your TACC password

    1. You should have chosen this when you signed up for your account. You can reset your password here if you have forgotten it.
  4. 2 factor authentication code

    1. This page describes the 2 factor authentication in general terms.

    2. This page is used to set it up for your account.

    3. This will either be displayed on the TACC app if you choose to install it on your phone, or will be sent to your phone via a text message after you enter your password.

The ssh command:

Once you have created your TACC userID and set up two-factor authentication, you should be ready to log in using the ssh command. The ssh command consists of 3 parts:

  1. The letters 'ssh' followed by a space.
    1. This is used to tell your computer what command you are trying to run.
  2. Your username followed by an @ symbol.
    1. This is used to tell the remote computer who is wanting access.
  3. The hostname/address of the remote computer you are trying to access.
    1. This is often very similar to a typical website address without any preceding http:// or www
    2. Alternatively this may be a numerical IP address.

Note that username@hostname has no spaces in it.

Logging in:

Type the following into your terminal window substituting your user name for "DED" in the example
ssh ded@stampede2.tacc.utexas.edu

Once you hit return, you will see a prompt for entering your password.

Many people get tripped up at this step as typing your password does not show any text causing people to think something has gone wrong. Your computer knows that you are typing a password which you want/need to keep secret and thus does not display any text as you type but does record the keys you enter. While the backspace key will work, most find it easier to simply hit return to get a new password prompt and try again if you make a mistake.

Next you will be prompted for your TACC Token Code. This will either be the number displayed on the TACC app if you chose to install it or the number you receive via text message.

Logging into remote computers

If this is the first time you are logging into stampede2 from the computer you are currently using, you will be issued a security warning. The same will be true the first time you log into any of the other TACC resource, or other remote computer. If you ever see a security warning logging into somewhere that you use commonly you should answer no and try to figure out why you were warned. Otherwise type "yes" to bypass the security check.

If you are successful you should see something that looks like this with some differences:

We will discuss several of the things shown in the terminal window during the class, but for now, you are all set.

Return to the GVA2022 main page.

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