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If your Windows version does not have ssh in Command Prompt or PowerShell:
More advanced options for those who want a full Linux environment on their Windows system:
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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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- Answer yes to the SSH security question prompt
- this will only be asked the 1st time you access ls6
- Enter the password associated with your TACC account
- for security reasons, your password characters will not be echoed to the screen
- Get your 2-factor authentication code from your phone's TACC Token app, and type it in
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If you're using PuTTY as your Terminal from Windows:
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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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Now execute the lines below to set up a login script, called ~/.bashrc. [ Note the tilde ( ~ ) is shorthand for "my Home directory". See See Linux fundamentals: pathname Pathname syntax ]
When you login via an interactive shell, a well-known script is executed to establish your favorite environment settings. The well-known filename is ~/.bashrc (or ~/.profile on some systems), which is specific to the bash shell.
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# show a long listing of all files in the current directory, including "dot files" that start with a period ls -la |
Read more about File attributes
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What's going on with chmod? The chmod 600 ~/.bashrc command marks the file as readable and writable only by you. |
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$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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The ln -s command creates a symbolic link, a shortcut to the linked file or directory.
Want to know where a link points to? Use ls with the -l (long listing) option.
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There's a lot of stuff here; let's look at just a few things.
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Environment variables
The login script sets several environment variables.
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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 directory).
To see the value of an environment variable, use the echo command, then the variable name after a dollar sign ( $ ):
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ls $CORENGS |
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Read more about Environment variables
Shell completion with Tab
You can use these environment variables to shorten typing, for example, to look at the contents of the shared /work/projects/BioITeam directory as shown below, using the magic Tab key to perform shell completion.
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# hit Tab once to expand the environment variable name
ls $BIW
# hit Tab again to expand the environment variable
ls $BIWORK/
# now hit Tab twice to see the contents of the directory
ls /work/projects/BioITeam/
# type "pr" and hit Tab again
ls /work/projects/BioITeam/pr
# type "co" and hit Tab again
ls /work/projects/BioITeam/projects/co
# type "Co" and hit Tab again
ls /work/projects/BioITeam/projects/courses/Co
# your command line should now look like this
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/
# now type "mi" and one Tab
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/mi
# your command line should now look like this
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/
# now hit Tab once
# There is no unambiguous match, so hit Tab again
# After hitting Tab twice you should see several filenames:
# fastqc/ small.bam small.fq small2.fq
# now type "sm" and one Tab
# your command line should now look like this
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small
# type a period (".") then hit Tab twice again
# You're narrowing down the choices -- you should see two filenames
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small
# small.bam small.fq
# finally, type "f" then hit Tab again. It should complete to this:
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small.fq |
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Extending the $PATH
When you type a command name the shell has to have some way of finding what program to run. The list of places (directories) where the shell looks is stored in the $PATH environment variable. You can see the entire list of locations by doing this:
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echo $PATH
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echo $PATH
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As you can see, there are a lot of locations on the $PATH.
Here's how the common login script adds your $HOMEthe ~/local/bin directory you created above, to the location list (we'll create that directory shortly), along with a special dot character ( . ) that means "here", or "whatever the current directory is". In the statement below, colon ( : ) separates directories in the list. (Read more about Pathname syntax)
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export PATH=.:$HOME/local/bin:$PATH |
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Setting up the friendly command prompt
The complicated looking if statement in SECTION 3 of your .bashrc sets up a friendly shell prompt that shows the current working directory. This is done by setting the special PS1 environment variable and including a special \w directive that the shell knows means "current directory".
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