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Table of Contents

Getting to a remote computer

The Terminal window

Macs and Linux have Terminal programs built-in – find it now on your computer
Windows needs help
- Putty – http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html
  - simple Terminal and file copy programs
  - download either the Putty installer (https://the.earth.li/~sgtatham/putty/latest/w64/putty-64bit-0.70-installer.msi)
    - or just putty.exe (terminal) and pscp.exe (secure copy client)
- 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 – http://www.cygwin.com/
  - A full Linux environment, including X-windows for running GUI programs remotely
  - Complicated to install

SSH

ssh is an executable program that runs on

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.

SSH

ssh is an executable program that runs on your local computer and allows you to connect securely to a remote computer. We're going to use ssh to access the Stampede2 Lonestar6 compute cluster at TACC (Texas Advanced Computing Center), where the remote host name is 5stampede2ls6.tacc.utexas.edu.

On Macs or Linux, you run ssh from a Terminal window. To invoke a Linux Terminal window if you have the Windows subsystem for Linux installed, double-click on the icon for the Linux distribution you installed (e.g. Ubuntu).

In your local Terminal windowIn your local Terminal window:

Code Block

language	bash
title	SSH to access lonestar5 Lonestar6 at TACC

ssh <your_TACC_userID>@ls5userID>@ls6.tacc.utexas.edu

...



# For example:
ssh abattenh@ls6.tacc.utexas.edu

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

Wait

for security reasons, your password characters will not be echoed to the screen

Get your 2-factor authentication code to arrive via SMS or from your phone's TACC Token app, then 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

The bash shell

You're now at a command line! It looks as if you're running directly on the remote computer, but really there are two programs communicating:

your local Terminal
the remote Shell shell

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 your typing 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 Removed

Tip

The bash command-line environment is extremely powerful, but also complex and unforgiving – a one-character mistake can make all the difference between a command that works and one that doesn't!

In spite of the hurdles, learning to get around the Linux command line will pay substantial dividends. A good place to start is with our Linux fundamentals wiki page.

Setting up your environment

Create some directories symbolic links

First create a few directories and links we will use (more on these later).

Tip
You can copy and paste these lines from the code block below into your Terminal window. Just make sure you hit Enter after the last line.

Create some symbolic links that will come in handy later:

Code Block

language	bash
title	Create symbolic directory links

cd 
ln -s -f $SCRATCH scratch
ln -s -f $WORK2 work2
ln -s -f /work2/projects/BioITeam
ln -s -f /work2/projects/BioITeam/projects/courses/Core_NGS_Tools CoreNGS

Tip

$WORK2 and $SCRATCH are TACC environment variables that refer to your Work2 and Scratch file system areas. To see the value of an environment variable, use the echo command:

Code Block

language	bash

echo $SCRATCH

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 Work2 and Scratch file system areas
Having these link shortcuts will help when you want to copy files to your Work2 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

...

Code Block

language	bash
title	Set up $HOME/local/bin directory

mkdir -p ~/local/bin
cd ~/local/bin
ln -s -f /work2/projects/BioITeam/common/bin/launcher_creator.py
ln -s -f /work2/projects/BioITeam/common/bin/launcher_maker.py

Tip

title	The tilde ( ~ ) character

The tilde character ( ~ ) is a pathname shortcut that means "home directory". We'll see more of it later.

$HOME is an environment variable set by TACC that also refers to your home directory.

Setup your login profile (~/.bashrc)

Now execute the lines below to set up a login script, called .bashrc

When you login via an interactive shell as you did above, a well-known script is executed by the shell to establish your favorite environment settings. We've set up a common login script for you to start with that will help you know where you are in the file system and make it easier to access some of our shared resources. To set it up, do the steps below:

Warning

If you already have a .bashrc set up, make a backup copy first.

Code Block

language	bash

cd
cp .bashrc .bashrc.beforeNGS

You can restore your original login script after this class is over.

Code Block

language	bash
title	Copy a pre-configured login script

cd
cp /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.stampede2  .bashrc
chmod 600 .bashrc

Expand

title	What is chmod doing?

What's going on with chmod?

The chmod 600 .bashrc command marks the file as readable and writable only by you.
The .bashrc script file will not be executed unless it has these exact permissions settings.
The well-known filename is .bashrc (or .profile on some systems), which is specific to the bash shell.

Since .bashrc is executed when you login, to ensure it is set up properly you should first log off stampede2 like this:

Code Block

language	bash
title	Log off Lonestar5

exit

Then log back in to stampede2.tacc.utexas.edu. This time your .bashrc will be executed and you should see a new shell prompt:

Code Block
stamp2:~$

The great thing about this prompt is that it always tells you where you are, which avoids having to issue the pwd (present working directory) command all the time. Execute these commands to see how the prompt reflects your current directory.

Code Block

language	bash

mkdir -p ~/tmp/a/b/c
cd ~/tmp/a/b/c

# Your prompt should look like this:
stamp2:~/tmp/a/b/c$

The prompt now tells you you are in the c sub-directory of the b sub-directory of the a sub-directory of the tmp sub-directory of your Home directory ( ~ ).

So why don't you see the .bashrc file you copied to your home directory? Because all files starting with a period (dot files) are hidden by default. To see them add the -a (all) option to ls:

Code Block

language	bash
title	How to see hidden files

cd
ls -a

To see even more detail, including file type and permissions and symbolic link targets, add the -l (long listing) switch:

Code Block

title	Long listing form of ls

ls -la

Tip

title	ll alias

Your new ~/.bashrc files defines a ll alias command, so when you type ll it is short for ls -la.

Details about your login script

We list the contents of your .bashrc login script to the Terminal with 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	List .bashrc file contents without pausing

cd
cat .bashrc

# or for larger files...
more .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) or look at parts of the file with head or tail.

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

...

Image Added

About the command line

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

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

Setting up your environment

Setup your login profile (~/.bashrc)

Now execute the lines below to set up a login script, called ~/.bashrc. [ Note the tilde ( ~ ) is shorthand for "my Home directory". See Linux fundamentals: 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.

We've pre-created a common login script for you that will help you know where you are in the file system and make it easier to access some of our shared resources. To set it up, perform the steps below:

Tip
You can copy and paste these lines from the code block below into your Terminal window. Just make sure you hit Enter after the last line.

Warning

If you already have a .bashrc set up, make a backup copy first.

Code Block

language	bash

cd
ls -la 
# Do you see a .bashrc file? If so, save it off
cp .bashrc .bashrc.beforeNGS

You can restore your original login script after this class is over.

If your Terminal has a dark background (e.g. black), copy this file:

Code Block

language	bash
title	Copy a pre-configured login script for dark background Terminals

cp /corral-repl/utexas/BioITeam/core_ngs_tools/login/bashrc.corengs.ls6.dark_bg  ~/.bashrc
chmod 600 ~/.bashrc

If your Terminal has a light background (e.g. white), copy this file:

Code Block

language	bash
title	Copy a pre-configured login script for light background Terminals

cp /corral-repl/utexas/BioITeam/core_ngs_tools/login/bashrc.corengs.ls6.light_bg  ~/.bashrc
chmod 600 ~/.bashrc

So why don't you see the .bashrc file you just copied when you do ls? Because all files starting with a period (dot files) are hidden by default. To see them add the -l (long listing) and -a (all) options to ls:

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

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}~/.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 "$__PERSONAL_PATH__" ]; then
  export __PERSONAL_PATH__=1
  # for NGS course
  export LANG="C"  # avoid the annoying Perl warnings on cds, etc.
  export PATH=.:$HOME/local/bin:$PATH
fi
# export ALLOCATION=UT-2015-05-18    # Group is G-816696
  export BIWORK=/work2/projects/BioITeam
  export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools
  export BI=/corral-repl/utexas/BioITeam
  export PATH=.:$HOME/local/bin:$PATH
# For better colors using a dark background terminalFor better colors using a dark background terminal, un-comment this line:
#export LS_COLORS=$LS_COLORS:'di=1;33:fi=01:ln=01;36:'
# For better colors using a white background terminal, un-comment this line:
##export  export LS_COLORS=$LS_COLORS:'di=1;3334:fi=01:ln=01;36:'
# For better colors using a white background terminal, un-comment this line:
#  export LS_COLORS=$LS_COLORS:'di=1;34:fi=01:ln=01;36:'
fi
########################export LANG="C"  # avoid the annoying Perl locale warnings 
export BIWORK=/work/projects/BioITeam
export CORENGS=$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 "$PS1" ]; then PS1='stamp2ls6:\w$ '; fi
##################################
# SECTION 4 -- Umask and aliases and umask
#alias ls="ls --color=always"
alias ll='"ls -la'"
alias lah="ls -lah"
alias lc="wc -l"
alias lhhexdump='lsod -A x -t x1z -lhv'
umask 002
#############################################
# Optional Startup Script tracking
if [ -n "$SHELL_STARTUP_DEBUG" ]; then DBG_ECHO "${DBG_INDENT}}"; fi

So what does the common login script do? A lot! Let's look at just a few of them.

the "she-bang"

The first line is the she-bang. Even though the expression is inside a shell comment (denoted by the # character), it tells the shell what program should execute this file – in this case, bash itself.

Code Block

language	bash
title	The "she-bang" line

#!/bin/bash

...

}}"; fi

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

Environment variables

The login script also sets an environment variable $BIWORK to point to the shared directory /work2/projects/BioITeam, and another environment variable $CORENGS to point to the specific sub-directory for our classsets several environment variables.

Code Block

language	bash
title	Setting environment variables to useful locations

export BIWORK=/work2work/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools

Environment variablesvariables are like variables in a other programming language 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 for BIWORK is the pathname /work/projects/BioITeam). Read more about environment variables here: More on environment variables.

...

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 /work2work/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 after typing $BIWORK/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 /work2work/projects/BioITeam/

# type "pr" and hit Tab again
ls /work2work/projects/BioITeam/pr

# type "co" and hit Tab again
ls /work2work/projects/BioITeam/projects/co

# type "Co" and hit Tab again
ls /work2work/projects/BioITeam/projects/courses/Co

# your command line should now look like this
ls /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools/

# now type "mi" and one Tab
ls /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools/mi
 
# your command line should now look like this
ls /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/

# now hit Tab once
# now hit Tab once
# the shell expands as far as it can unambiguously,
# soThere 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 /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small

# now hit Tab twice
# You should see 3 filenames, all starting with "small"

/misc/small
 
# type a period (".") then hit Tab twice again
# You're narrowing down the choices -- you should see two filenames
ls /work2work/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 /work2work/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.

Here's how the common login script adds your $HOMEthe ~/local/bin directory you created above, to the location list – recall that's where we linked several useful scripts – , along with a special dot character ( . ) that means "here", or "whatever the current directory is". In the statment statement below, colon ( : ) separates directories in the list. (Read more about Pathname syntax)

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 "$PS1" ]; then PS1='ls5ls6:\w$ '; fi

Versions Compared

Old Version 152

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Key

Getting to a remote computer

The Terminal window

SSH

Getting to a remote computer

The Terminal window

SSH

The bash shell

Setting up your environment

Create some directories symbolic links

Setup your login profile (~/.bashrc)

Details about your login script

About the command line

Setting up your environment

Setup your login profile (~/.bashrc)

Create some symbolic links and directories

Details about your login script

the "she-bang"

Environment variables

Shell completion with Tab

Extending the $PATH

Setting up the friendly command prompt