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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.

Tutorial Objectives:

1. Ensure "OpenSSH Client" is activated on your computer
2. Launch powershell command line interface.
3. Use ssh command to log into lonestar5 on TACC.

Launching powershell Image Modified: 

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powershell powershell

Use one of the following to launch the powershell application:

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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.

Good response showing ssh command is working and you can continue to use the ssh command to log into lonestar5:

Bad response showing you need to check the alternative program or skip down to the troubleshooting section:

Use ssh command to log into lonestar5: 

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ssh_command ssh_command

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

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ssh ded@ls5.tacc.utexas.edu

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If you see a screen like the above, you can Return to the GVA2020 main page.

Troubleshooting ssh command:

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Troubleshooting Troubleshooting

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 show up for one of the zoom help sessions or email your instructor to set up an alternate time.

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1. click "Add a feature" near the top. 
2. On the subsequent screen you should see OpenSSH client listed there with an option to install it once you click it.
3. Restart your computer once the installation is complete.
4. Retry launching the powershell application and retry the ssh command from above.

Check for alternate powershell.exe programs:

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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 show up during one of the scheduled zoom times or via email to schedule an additional time.

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.

Return to the GVA2020 main page.

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