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title	Other Windows ssh/Terminal options

If your Windows version does not have ssh in Command Prompt or PowerShell:

Download the free PuTTY suite of remote access tools, which includes a nice Terminal program: https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html.
- Either the Putty installer or just putty.exe (Terminal) and pscp.exe (secure copy client)

More advanced options for those who want a full Linux environment on their Windows system:

Windows Subsystem for Linux – Windows 10 Professional includes a Ubuntu-like bash shells
- See https://docs.microsoft.com/en-us/windows/wsl/install-win10
- We recommend the Ubuntu Linux distribution, but any Linux distribution will have an SSH client

From now on, when we refer to "Terminal", it is either the Mac/Linux Terminal program, Windows Command Prompt or PowerShell, or the PuTTY program.

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There are many shell programs available in Linux, but the default is bash (Bourne-again shellBourne-again shell).

The Terminal is pretty "dumb" – just sending what you type over its secure sockets layer (SSL) connection to TACC, then displaying the text sent back by the shell. The real work is being done on the remote computer, by executable programs called by the bash shell (also called commands, since you call them on the command line).

About the command line

Read more about the command line and commands on our Linux fundamentals page:

The bash shell REPL and commands
Linux fundamentals: Getting help
Linux fundamentals: Literal characters and metacharacters
About command line input

Setting up your environment

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Tip
$WORK and $SCRATCH are TACC environment variables that refer to your Work and Scratch file system areas (– more on these file system areas soon. (Read more about Environment variables).

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title	What is "ln -s" doing?

The ln -s command creates a symbolic link, a shortcut to the linked file or directory.

Here the link targets are your Work and Scratch file system areas
Having these link shortcuts will help when you want to copy files to your Work or Scratch, and when you navigate the TACC file system using a remote SFTP client
Always change directory (cd) to the directory where we want the links created before executing ln -s
- Here we want the links under your home directory (cd with no arguments)

Want to know where a link points to? Use ls with the -l (long listing) option.

Code Block

language	bash
title	ls -l shows where links go

ls -l

AnchorLocal_Bin_SetupLocal_Bin_SetupSet up a ~/local/bin directory and link a script there that we will use in the class.

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They have a name (like BIWORK above) and a value (the value of $BIWORK is the pathname of the shared /work/projects/BioITeam directory). See More on environment variables.

To see the value of an environment variable, use the echo command, then the variable name after a dollar sign ( $ ):

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Code Block

language	bash

ls $CORENGS

(Read more about Environment variables)

Shell completion with Tab

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Key

About the command line

Setting up your environment

Shell completion with Tab