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Table of Contents

Getting to a remote computer

The Terminal window

Macs and Linux have a Terminal program built-in – find it now on your computer
Windows 10 or later has ssh and scp in Command Prompt or PowerShell (may require latest Windows updates)
- Open the Start menu → Search for Command

...

Table of Contents

Getting to a remote computer

The Terminal window

Macs and Linux have a Terminal program built-in – find it now on your computer
Windows 10 or later has ssh and scp in Command Prompt or PowerShell (may require latest Windows updates)
- Open the Start menu → Search for Command

Expand

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

...

Cygwin (https://www.cygwin.com/)
- Includes an X-Windows server and an X11-enabled XTerm that can be installed

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.

...

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

Expand

title	Logging in with PuTTY

If you're using PuTTY as your Terminal from Windows:

Double-click the Putty icon
In the PuTTY Configuration window
- make sure the Connection type is SSH
- enter ls6.tacc.utexas.edu for Host Name
  - Optional: to save this configuration for further use:
    - Enter Lonestar6 into the Saved Sessions text box, then click Save
    - Next time select Lonestar6 from the Saved Sessions list and click Load.
- click Open button
- answer Yes to the SSH security question
In the PuTTY terminal
- enter your TACC user id after the "login as:" prompt, then Enter
- enter the password associated with your TACC account
- provide your 2-factor authentication code

...

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).

Image RemovedImage Added

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

...

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.

...

Code Block

language	bash

# show a long listing of all files in the current directory, including "dot files" that start with a period
ls -la

Expand

Details about your login script

Let's take a look at the contents of your ~/.bashrc login script, using the cat (concatenate files) command. cat simply reads a file and writes each line of content to standard output (here, your Terminal):

Code Block

language	bash
title	Display .bashrc file contents

cd  
cat .bashrc

Tip

title	Don't use cat for large files

The cat command just displays the entire file's content, line by line, without pausing, so should not be used to display large files. Instead, use a pager like more or less. For example:

more ~/.bashrc

This will display one "page" (Terminal screen) of text at a time, then pause. Press space to advance to the next page, or Ctrl-c to exit more.

You'll see the following (you may need to scroll up a bit to see the beginning):

...

language	bash
title	Contents of your .bashrc file

...

Create some symbolic links and directories

Create some symbolic links that will come in handy later:

Code Block

language	bash
title	Create symbolic directory links

cd  # makes your Home directory the "current directory"
ln -s -f $SCRATCH scratch
ln -s -f $WORK work
ln -sf /work/projects/BioITeam/projects/courses/Core_NGS_Tools CoreNGS

ls # you'll see the 3 symbolic links you just created

Symbolic links (a.k.a. symlinks) are "pointers" to files or directories elsewhere in the file system hierarchy. You can almost always treat a symlink as if it is the actual file or directory.

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)

Unlink

Expand

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

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

Code Block

language	bash
title	Set up ~/local/bin directory

mkdir -p ~/local/bin
cd ~/local/bin
ln -s -f /work/projects/BioITeam/common/bin/launcher_creator.py

Since our ~/.bashrc login script added ~/local/bin to our $PATH, we can call any script or command in that directory with just its file name. And Tab completion works on program names too:

Code Block

language	bash

cd

# hit Tab once after typing "laun"
# This will expand to launcher_creator.py

Details about your login script

Let's take a look at the contents of your ~/.bashrc login script, using the cat (concatenate files) command. cat simply reads a file and writes each line of content to standard output (here, your Terminal):

Code Block

language	bash
title	Display .bashrc file contents

cd  
cat .bashrc

Tip

title	Don't use cat for large files

The cat command just displays the entire file's content, line by line, without pausing, so should not be used to display large files. Instead, use a pager like more or less. For example:

more ~/.bashrc

This will display one "page" (Terminal screen) of text at a time, then pause. Press space to advance to the next page, or Ctrl-c to exit more.

You'll see the following (you may need to scroll up a bit to see the beginning):

Code Block

language	bash
title	Contents of your .bashrc file

#!/bin/bash
# TACC startup script: ~/.bashrc version 2.1 -- 12/17/2013
#   This file is NOT automatically sourced for login shells.
# Your ~/.profile can and should "source" this file.
# Note neither ~/.profile nor ~/.bashrc are sourced automatically
# by bash scripts.
#   In a parallel mpi job, this file (~/.bashrc) is sourced on every
# node so it is important that actions here not tax the file system.
# Each nodes' environment during an MPI job has ENVIRONMENT set to
# "BATCH" and the prompt variable PS1 empty.
#################################################################
# Optional Startup Script tracking. Normally DBG_ECHO does nothing
if [ -n "$SHELL_STARTUP_DEBUG" ]; then DBG_ECHO "${DBG_INDENT}}"; fi

There's a lot of stuff here; let's look at just a few things.

environment variables

The login script sets several environment variables.

Code Block

language	bash
title	Setting environment variables to useful locations

export BIWORK=/work/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools

Environment variables are like variables in other programming languages like python or perl (in fact bash is a complete programming language).

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 ( $ ):

Code Block

language	bash

echo $CORENGS

We'll use the $CORENGS environment variable to avoid typing out a long pathname:

Code Block

language	bash

ls $CORENGS

shell completion

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.

Tip

title	Important Tip -- the Tab key is your BFF!

The Tab key is one of your best friends in Linux. Hitting it invokes shell completion, which is as close to magic as it gets!

Tab once will expand the current command line contents as far as it can unambiguously.
- if nothing shows up, there is no unambiguous match
Tab twice will give you a list of everything the shell finds matching the current command line.
- you then decide where to go next

Follow along with this:

Code Block

language	bash
title	Shell completion exercise

# 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/~/.bashrc{"; fi
##########
# SECTION 1 -- modules
if [ -z "$__BASHRC_SOURCED__" -a "$ENVIRONMENT" != BATCH ]; then
  export __BASHRC_SOURCED__=1
  module load launcher
fi
############
# SECTION 2 -- environment variables
if [ -z "$__PERSONAL_PATH__" ]; then
  export __PERSONAL_PATH__=1
  export PATH=.:$HOME/local/bin:$PATH
fi
# For better colors using a dark background terminal, un-comment this line:
#export LS_COLORS=$LS_COLORS:'di=1;33:fi=01:ln=01;36:'
# For better colors using a white background terminal, un-comment this line:
#export LS_COLORS=$LS_COLORS:'di=1;34:fi=01:ln=01;36:'
export LANG="C"  # avoid the annoying Perl locale warnings 
export BIWORK=/work/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools
export BI=/corral-repl/utexas/BioITeam
export ALLOCATION=OTH21164        # For ls6        Group is G-824651
##export ALLOCATION=UT-2015-05-18 # For stampede2  Group is G-816696

##########
# SECTION 3 -- controlling the prompt
if [ -n "$PS1" ]; then PS1='ls6:\w$ '; fi
##########
# SECTION 4 -- Umask and aliases
#alias ls="ls --color=always"
alias ll="ls -la"
alias lah="ls -lah"
alias lc="wc -l"
alias hexdump='od -A x -t x1z -v'
umask 002
##########
# Optional Startup Script tracking
if [ -n "$SHELL_STARTUP_DEBUG" ]; then DBG_ECHO "${DBG_INDENT}}"; fi

There's a lot of stuff here; let's look at just a few things.

Environment variables

The login script sets several environment variables.

Code Block

language	bash
title	Setting environment variables to useful locations

export BIWORK=/work/projects/BioITeam
export CORENGS=$BIWORK/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

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:

Code Block

language	bash
title	See where the bash shell looks for programs

echo $PATH

As you can see, there are a lot of locations on the $PATH. That's because when you load modules at TACC (such as the module load lines in the common login script), that makes the programs available to you by putting their installation directories on your $PATH. We'll learn more about modules later.

Here's how the common login script adds your $HOME/local/bin directory 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.

Code Block

language	bash
title	Adding directories to PATH

export PATH=.:$HOME/local/bin:$PATH

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".

Code Block

language	bash
title	Setting up the friendly shell prompt for stampede

##########
# SECTION 3 -- controlling the prompt
if [ -n "$PS1" ]; then PS1='ls6:\w$ '; fi

Create some symbolic links and directories

Create some symbolic links that will come in handy later:

Code Block

language	bash
title	Create symbolic directory links

cd  # makes your Home directory the "current directory"
ln -s -f $SCRATCH scratch
ln -s -f $WORK work
ln -sf

Environment variables are like variables in other programming languages like python or perl (in fact bash is a complete programming language).

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

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

Code Block

language	bash

echo $CORENGS

We'll use the $CORENGS environment variable to avoid typing out a long pathname:

Code Block

language	bash

ls $CORENGS

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.

Tip

title	Important Tip -- the Tab key is your BFF!

The Tab key is one of your best friends in Linux. Hitting it invokes shell completion, which is as close to magic as it gets!

Tab once will expand the current command line contents as far as it can unambiguously.
- if nothing shows up, there is no unambiguous match
Tab twice will give you a list of everything the shell finds matching the current command line.
- you then decide where to go next

Follow along with this:

Code Block

language	bash
title	Shell completion exercise

# 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
CoreNGS 
ls # you'llyour seecommand theline 3should symbolicnow linkslook youlike justthis
created

Symbolic links (a.k.a. symlinks) are "pointers" to files or directories elsewhere in the file system hierarchy. You can almost always treat a symlink as if it is the actual file or directory.

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).

Expand

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.

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

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:

Code Block

title
language	bash

ls -l shows where links go

ls -l

...

See where the bash shell looks for programs

echo $PATH

As you can see, there are a lot of locations on the $PATH.

Here's how the common login script adds the ~/local/bin directory and link a script there that we will use in the class.

...

you created above, to the location list, 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)

mkdir -p ~

Code Block

language	bash
title	Set up ~/local/bin directory

Adding directories to PATH

export PATH=.:$HOME/local/bin
cd ~/local/bin
ln -s -f /work/projects/BioITeam/common/bin/launcher_creator.py

Since our ~/.bashrc login script added ~/local/bin to our $PATH, we can call any script or command in that directory with just its file name. And Tab completion works on program names too:

Code Block

language	bash

cd

# hit Tab once after typing "laun"
# This will expand to launcher_creator.py

About command line input

You know the command line is ready for input when you see the command line prompt.

Like everything in Unix, the command line has similarities to a text file. And in Unix, all text file "lines" are terminated by a linefeed character (\n, also called a newline).

Expand

title	Line ending differences...

Note: The Unix linefeed (\n) line delimiter is different from Windows, where the default line ending is carriage-return + linefeed (\r\n), and some Mac text editors that just use a carriage return (\r).

As mentioned earlier, the shell executes command line input when it sees a linefeed, which happens when you press Enter after entering the command.

But you can enter more than one command on a single line – just separate the commands with a semi-colon ( ; ).

Code Block

language	bash
title	Multiple command on a line

cd; ls -lh

You can also split a single command across multiple lines by adding a backslash ( \ ) at the end of the line you want to continue, before pressing Enter.

Code Block

language	bash
title	Split a command across multiple lines

ls6:~$ ls ~/.bashrc \
> ~/.profile

Notice that the shell indicates that it is not done with command-line input by displaying a greater than sign ( > ). You just enter more text then Enter when done.

Tip

title	Use Ctrl-C to exit the current command input

At any time during command input, whether on the 1st command line prompt or at a > continuation, you can press Ctrl-c (Control key and the c key at the same time) to get back to the command prompt.

Command input errors

You don't always type in commands, options and arguments correctly – you can misspell a command name, forget to type a space, specify an unsupported option or a non-existent file, or make all kinds of other mistakes.

What happens? The shell attempts to guess what kind of error it is and reports an appropriate error message as best it can.

Some examples:

Code Block

language	bash

# You type the name of a command that is not installed on your system
ls6:~$ lz  
Command 'lz' not found, but can be installed with:
apt install mtools
Please ask your administrator.

# You enter something that is close to an existing, or known, command
ls6:~$ catt
Command 'catt' not found, did you mean:
  command 'cat' from deb coreutils (8.30-3ubuntu2)
  command 'catty' from deb node-catty (0.0.8-1)
  command 'ratt' from deb ratt (0.0~git20180127.c44413c-2)
Try: apt install <deb name>

# You try to use an unsupported option
ls6:~$ ls -z
ls: invalid option -- 'z'
Try 'ls --help' for more information.

# You specify the name of a file that does not exist
ls6:~$ ls xxx
ls: cannot access 'xxx': No such file or directory:$PATH

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".

Code Block

language	bash
title	Setting up the friendly shell prompt for stampede

##########
# SECTION 3 -- controlling the prompt
if [ -n "$PS1" ]; then PS1='ls6:\w$ '; fi

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Key

Getting to a remote computer

The Terminal window

Getting to a remote computer

The Terminal window

About the command line

Setting up your environment

Details about your login script

Create some symbolic links and directories

Details about your login script

environment variables

shell completion

Environment variables

extending the $PATH

setting up the friendly command prompt

Create some symbolic links and directories

Shell completion with Tab

Extending the $PATH

About command line input

Command input errors

Setting up the friendly command prompt