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. Windows10 began including an "OpenSSH Client" package first as an optional feature before enabling by default. Installation of this feature enables access to some key commands on the windows command line, or power shell application. If you are already experienced with logging into remote computers on the command line via other programs, it is recommended that you continue to us those programs, but please note support may be more limited.
- Ensure "OpenSSH Client" is activated on your computer
- Launch powershell command line interface.
- Use ssh command to log into stampede2 on TACC.
Use one of the following to launch the powershell application:
- hit the windows key on your keyboard and type out powershell
- On the start menu expand "Windows PowerShell"
In either case you may see 2 versions. 1 titled "Windows PowerShell" and 2 titled "Windows PowerShell (x86)". On my wife's computer, the "correct" one is the one that lacks the (x86). You may need to experiment with both by typing ssh and seeing what happens. In either case feedback to the instructor of what worked for you may help make this more straight forward for future students.
Use ssh command to log into stampede2:
You will need 4 pieces of information to log into stampede2:
Your TACC userID
Hostname of the remote computer you are trying to log into
For this class the hostname will be "stampede2.tacc.utexas.edu" for stampede2.
Your TACC password
- You should have chosen this when you signed up for your account. You can reset your password here if you have forgotten it.
2 factor authentication code
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:
The ssh command consists of 3 parts:
- The letters 'ssh' followed by a space.
- This is used to tell your computer what command you are trying to run.
- Your username followed by an @ symbol.
- This is used to tell the remote computer who is wanting access.
- The hostname/address of the remote computer you are trying to access.
- This is often very similar to a typical website address without any preceding http:// or www
- Alternatively this may be a numerical IP address.
Note that username@hostname has no spaces in it.
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 followed by additional information:
If you see a screen like the above, you can Return to the GVA2022 main page.
Troubleshooting ssh command:
It is strongly suggested that you verify the installation of the openssh client before checking for alternate powershell applications. If you have tried both of these troubleshooting options and are still having trouble please email your instructor to set up a time for a zoom session to troubleshoot.
Verify "OpenSSH Client" is installed:
Navigate through the following:
- Windows settings
- Optional Features
Scrolling down you should see an optional feature titled "OpenSSH Client". Note that this is different than "OpenSSH Server" which is not enabled by default and will not be needed for anything in this course.
If you do not see "OpenSSH Client" in optional features:
- click "Add a feature" near the top.
- On the subsequent screen you should see OpenSSH client listed there with an option to install it once you click it.
- Restart your computer once the installation is complete.
- Retry launching the powershell application and retry the ssh command from above.
Check for alternate powershell.exe programs:
Navigate through the following in the windows file explorer:
- "C" drive (or other drive containing your windows installation)
- "Windows" folder
- "System32" folder (note this is different than the "System" folder which may also be present)
Verify that there is a folder titled "OpenSSH". Should be if installation was successful above.
Inside of the System32 folder, enter powershell.exe in the search bar near the top right corner of the window.
If it returns a result, launch that instance of powershell and retry the ssh command from above.
Contact instructor via scheduled zoom time or email:
If both of the troubleshooting steps above failed, please email to schedule a zoom session.
Windows10 OpenSSH alternatives:
As alluded to above, it is a relatively recent change by Microsoft/windows to recognize the usefulness of having an ssh client built into the operating system. As such, multiple alternatives exist for ssh clients. While the commands in this class will be centered around the powershell environment with OpenSSH enabled, in your future work you may decide to branch out into alternatives. If you are already familiar with an alternative program, you are encouraged to continue using it.
At the end of the class several alternatives will be listed here with links for your future consideration.