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The Terminal window

• Macs and Linux have a Terminal programs program 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 putty.exe (terminal) and pscp.exe (secure copy client)
  • Git-bash – http://msysgit.github.io/
    • terminal plus minimal Linux environment
  • Cygwin – http://www.cygwin.com/
    
    • a full Linux environment, including X-windows for running GUI programs remotely
    • complicated to install
  10 or later has ssh and scp in Command Prompt or PowerShell (may require latest Windows updates)
  • Open the Start menu → Search for Command
    

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 Lonestar6 compute cluster at TACC (Texas Advanced Computing Center), where the remote host name is ls6.tacc.utexas.edu.

In your local Terminal window:On Macs, Linux and Windows Git-bash or Cygwin, you run it from a Terminal window. Answer yes to the SSH security question prompt.

ssh your<your_TACC_userID@stampedeuserID>@ls6.tacc.utexas.edu

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

...

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

• Answer yes for Host Name
• click Open button
answer Yes to the SSH security question prompt
• In the PuTTY terminal
  • enter your TACC user id after the login as: prompt, then Enter

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 and the remote Shell. There are many shell programs available in Linux, but the default is bash (Bourne-again shell). The Terminal is pretty "dumb" – just sending your typing 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 programs called by the bash shell.

Image Removed

Setting up your environment

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
cd ln -s -f $SCRATCH scratch ln -s -f $WORK work ln -s -f /corral-repl/utexas/BioITeam

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

Warning
If you already have a local sub-directory in your $HOME directory, rename it temporarily. You can restore it after the class is over. Code Block language bash cd mv local local.bak

Code Block
language bash
mkdir -p $HOME/local/bin cd $HOME/local/bin ln -s -f /corral-repl/utexas/BioITeam/bin/launcher_creator.py ln -s -f /work/01063/abattenh/local/bin/cutadapt ln -s -f /work/01063/abattenh/local/bin/samstat

Expand
title What's going on?
What's going on? The mkdir command creates a new directory. The -p option says to create intermediate directories if needed (like local here). here we're creating a $HOME/local/bin directory where we'll put some programs used in the course $HOME is an environment variable set by TACC that refers to your home directory. The ln -s command creates a symbolic link, a shortcut the the linked file or directory. here the link targets are programs we want – instead of copying the programs, we just link to them always change directory (cd) to the directory where we want the links created before executing ln -s here we want the links in $HOME/local/bin Want to know more about a Linux command? Type the command name then the --help option. For example, with mkdir: Code Block language bash title One way to get help mkdir --help

Now execute the lines below to set up a login script, called .profile_user. Whenever 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 profile 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 up this profile, do the steps below:

...

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

Code Block
language bash
cd cp .profile_user .profile_user.bak

• • 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

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:

1. your local Terminal
2. the remote shell

There are many shell programs available in Linux, but the default is bash (Bourne-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 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 profilescript for light background Terminals
cd cp /corral-repl/utexas/BioITeam/core_ngs_tools/common/stampede_dircolors .dircolors cp /corral-repl/utexas/BioITeam/core_ngs_tools/common/core_ngs_profile .profile_userlogin/bashrc.corengs.ls6.light_bg ~/.bashrc chmod 600 ~/.profile_user

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

...

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 title How to log off Stampede
exit

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

Code Block
stamp:~$

# 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)

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.

Since your ~/.bashrc is executed when you login, to ensure it is set up properly you should first log off Lonestar6 like thisThe 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
stamp:~$ mkdir -p tmp/a/b/c stamp:~$ cd tmp/a/b/c stamp:~/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 ( ~ ).

Expand
title What's that ~ character?
The tilde character ( ~ ) is a shortcut that means "home directory". We'll see more of it later.

 

Your profile has also installed nice directory colors, which you can see when you list your home directory:

Code Block
language bash
cd ls

So why don't you see the .profile_user 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
ls -a

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

Code Block
title Long listing form of ls
ls -la

Details about your login profile

We list its content to the Terminal with the cat (concatenate files) command:

Code Block
cat .profile_user

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

Code Block
title Contents of your .profile_user file
#!/bin/bash # Change the command line prompt to contain the current directory path if [ "$TACC_SYSTEM" == "stampede" ]; then PS1='stamp:\w$ ' else PS1='lstar:\w$ ' fi # Try to ensure all created files can be read/writtin by group members umask 002 # Make common, useful software always available module load python; module load launcher # Set the default project allocation for launcher_creator.py export ALLOCATION=genomeAnalysis # Environment variables for useful locations export BI=/corral-repl/utexas/BioITeam export CLASSDIR="$BI/core_ngs_tools" # Add current directory and $HOME/local/bin to PATH export PATH=.:$HOME/local/bin:$PATH # Use yellow for directories, not that horrible blue dircolors .dircolors > /dev/null

So what does the common profile file do? Several things. Let's look at a few of them.

the "she-bang"

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

Code Block
title The "she-bang" line
#!/bin/bash

environment variables

The profile also sets an environment variable named BI to point to the shared directory: /corral-repl/utexas/BioITeam, and another environment variable named CLASSDIR to point to the specific sub-directory for our class.

Code Block
title Setting environment variables for common paths
# Environment variables for useful locations export BI=/corral-repl/utexas/BioITeam export CLASSDIR="$BI/core_ngs_tools"

Environment variables are like variables in a programming language like python or perl (in fact bash is a complete programming language). They have a name (like BI above) and a value (the value for BI is the pathname /corral-repl/utexas/BioITeam).

More on environment variables

shell completion

You can use these environment variables to shorten typing, for example, to look at the contents of the shared BioITeam directory as shown below.

title Log off Lonestar6

exit

Your Terminal  has logged off of Lonestar6 and is back on your local computer.

Now log back in to ls6.tacc.utexas.edu. This time your ~/.bashrc will be executed to establish your environment:

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

You should see a new command line prompt:

Code Block
ls6:~$

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

Code Block
language bash
# mkdir -p says to create all parent directories in the specified path mkdir -p ~/tmp/a/b/c cd ~/tmp/a/b/c # Your prompt should look like this: ls6:~/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 ( ~ ).

Your login script has configured this command prompt behavior, along with a number of other things.

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)




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
Code Block
title Shell completion exercise
# hit Tab once after typing $BI/ to expand the environment variable ls $BI/ "laun" # nowThis hitwill Tab twiceexpand to see the contents of the directory ls /corral-repl/utexas/BioITeam/ # now type "co" and hit Tab again ls /corral-repl/utexas/BioITeam/co # your command line should now look like this ls /corral-repl/utexas/BioITeam/core_nge_tools/ # now type "m" and one Tab ls /corral-repl/utexas/BioITeam/core_nge_tools/m # now just type one Tab ls /corral-repl/utexas/BioITeam/core_nge_tools/misc/ # the shell expands as far as it can unambiguously, so your command line should look like this ls /corral-repl/utexas/BioITeam/core_nge_tools/misc/small # type a period (".") then hit Tab twice again -- you're narrowing down the choices ls /corral-repl/utexas/BioITeam/core_nge_tools/misc/small. # finally, hit Tab twice to see possible completions now -- you should see two filenames

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

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 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 profile), that mechanism makes the programs available to you by putting their installation directories on your $PATH. We'll learn more about modules shortly.

Here's how the shared profile adds your $HOME/local/bin directory to the location list – recall that's where we linked some programs we'll use – along with a special dot character ( . ) that means "here", or "whatever the current directory is".

Code Block
language bash title Adding directories to PATH
# Add current directory and $HOME/local/bin to PATH export PATH=.:$HOME/local/bin:$PATH

setting up the friendly command prompt

The complicated looking if statement near the top of your profile is checking whether you're on stampede or lonestar (this .profile_user works on both), and setting up your friendly shell prompt so that it includes 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
title Setting up the friendly shell prompt for stampede or lonestar
# Change the command line prompt to contain the current directory path if [ "$TACC_SYSTEM" == "stampede" ]; then PS1='stamp:\w$ ' else PS1='lstar:\w$ ' fi

File systems at TACC

Local file systems

There are 3 local file systems available on any TACC cluster (stampede, lonestar, etc.), each with different characteristics. All these local file systems are very fast and set up for parallel I/O (Lustre file system).

On stampede these local file systems have the following characteristics:

	Home	Work	Scratch
quota	5 GB	400 GB	12+ PB (basically infinite)
policy	backed up	not backed up, not purged	not backed up, purged if not accessed recently (~10 days)
access command	cd	cdw	cds
environment variable	$HOME	$WORK	$SCRATCH
root file system	/home	/work	/scratch
use for	Small files such as scripts that you don't want to lose.	Medium-sized artifacts you don't want to copy over all the time. For example, custom programs you install (these can get large), or annotation file used for analysis.	Large files accessed from batch jobs. Your starting files will be copied here from somewhere else, and your results files will be copied back to your home system.

When you first login, the system gives you information about disk quota and your compute allocation quota:

Code Block

--------------------- Project balances for user abattenh ---------------------- | Name Avail SUs Expires | Name Avail SUs Expires | | CancerGenetics 121912 2014-09-30 | genomeAnalysis 99902 2015-03-31 | ------------------------ Disk quotas for user abattenh ------------------------ | Disk Usage (GB) Limit %Used File Usage Limit %Used | | /home1 0.0 5.0 0.02 251 150000 0.17 | | /work 1.5 1024.0 0.15 2612 3000000 0.09 | -------------------------------------------------------------------------------

changing TACC directories


When you first login, you start in your home directory. Use these commands to change to your other file systems. Notice how your command prompt helpfully changes to show your location.

Code Block
language bash
cdw cds cd

Tip
The cd (change directory) command with no arguments takes you to your home directory on any Linux/Unix system. The cdw and cds commands are specific to the TACC environment.

Corral

Corral is a gigantic (multiple PB) storage system (spinning disk) where researchers can store data. UT researchers may request up to 5 TB of corral storage through the normal TACC allocation request process. Additional space on corral can be rented for ~$210/TB/year.

The UT/Austin BioInformatics Team, a loose group of researchers, maintains a common directory area on corral.

Code Block
language bash
ls /corral-repl/utexas/BioITeam

File we will use in this course are in a subdirectory there:

Code Block
language bash
ls /corral-repl/utexas/BioITeam/core_ngs_tools

A couple of things to keep in mind regarding corral:

• corral is a great place to store data in between analyses.
  • Copy your data from corral to $SCRATCH
  • Run your analysis batch job
  • Copy your results back to corral
• On stampede you can access corral directories from login nodes (like the one you're on now), but your batch jobs cannot access it.
  • This is because corral is a network file system, like Samba or NFS.
  • Since stampede has so many compute nodes, it doesn't have the network bandwidth that would allow simultaneous access to corral .
• Occasionally corral can become unavailable. This can cause any command to hang that tries to access corral data.

Ranch

Ranch is a gigantic (multiple PB) tape archive system where researchers can archive data. UT researchers may request large (multi-TB) ranch storage allocations through the normal TACC allocation request process.

There is currently no charge for ranch storage. However, since the data is stored on tape it is not immediately available – robots find and mount appropriate tapes when the data is requested, and it can take minutes to hours for the data to appear on disk. (The metadata about your data – the directory structures and file names – is always accessible, but the actual data in the files is not on disk until "staged". See the ranch user guide for more information: https://www.tacc.utexas.edu/user-services/user-guides/ranch-user-guide.

Once that data is staged to the ranch disk it can be copied to other places. However, the ranch file system is not mounted as a local file system from the stampede or lonestar clusters. So remote copy commands are needed to copy data to and from ranch (e.g. scp, sftp, rsync).

Staging your data

So, your sequencing center has some data for you. They may send you a list of web links to use to download the data, or if you're a GSAF customer with an account on fourierseq.icmb.utexas.edu, you'll receive the name of a directory to access.

The first task is to get this data to a permanent storage area. This should not be your laptop or one of the TACC local file systems! Corral is a great place for it, or a server maintained by your Lab or company.

We're going to pretend – just for the sake of this class – that your permanent storage area is in your TACC work area. Execute these commands to make your "archive" directory and some sub-directories.

Code Block
language bash
mkdir -p $WORK/archive/original/2014_05.core_ngs

Here's an example of a "best practice". Wherever your permanent storage area is, it should have a rational sub-directory structure that reflects its contents. It's easy to process a few NGS datasets, but when they start multiplying like tribbles, good organization and naming conventions will be the only thing standing between you and utter chaos!

For example:

• original – for original sequencing data (compressed fastq files)
  • subdirectories named by year_month.<project or purpose>
• aligned – for alignment artifacts (bam files, etc)
  • subdirectories named by year_month.<project or purpose>
• analysis – further downstream analysis
  • reasonably named subdirectories, often by project
• genome – reference genomes and other annotation files used in alignment and analysis
  
  • subdirectories for different reference genomes
  • e.g. ucsc/hg19, ucsc/sacCer3, mirbase/v20
• code – for scripts and programs you and others in your organization write
  • ideally maintained in a version control system such as git, subversion or cvs.
  • easiest to name sub-directories for people.

Download from a link – wget

Well, you don't have a desktop at TACC to "Save as" to, so what to do with a link? The wget program knows how to access web URLs such as http, https and ftp.

...

wget

Get ready to run wget from the directory where you want to put the data. Don't press Enter after the wget command – just put a space after it.

Code Block
language bash
cd $WORK/archive/original/2014_05.yeast wget

Here are two web links:

• http://web.corral.tacc.utexas.edu/BioITeam/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
• http://web.corral.tacc.utexas.edu/BioITeam/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz

Right click on the 1st link in your browser, then select "Copy link location" from the menu. Now go back to your Terminal. Put your cursor after the space following the wget command then either right-click, or Paste. The command line to be executed should look like this:

Code Block
language bash
wget http://web.corral.tacc.utexas.edu/BioITeam/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz

Now press Enter to get the command going. Repeat for the 2nd link.

Copy from a corral location - cp or rsync

Suppose you have a corral allocation where your organization keeps its data, and that the sequencing data has been downloaded there. You can use various Linux commands to copy the data locally from there to your $SCRATCH area.

cp

The cp command copies one or more files from a local source to a local destination. It has the most common form:

cp [options] <source file 1> <source file 2> ... <destination directory>

Make a directory in your scratch area and copy a single file to it. The trailing slash ("/") on the destination says it is a directory.

Code Block
language bash title cp - single file copy
mkdir -p $SCRATCH/data/test1 cp /corral-repl/utexas/BioITeam/web/tacc.genomics.modules $SCRATCH/data/test1/ ls $SCRATCH/data/test1

Copy a directory to your scratch area. The -r argument says "recursive".

Code Block
language bash title cp - directory copy
cds cd data cp -r /corral-repl/utexas/BioITeam/web/general/ general/

Exercise: What files were copied over?

Expand
title Hint
ls general

Expand
title Answer
BEDTools-User-Manual.v4.pdf  SAM1.pdf  SAM1.v1.4.pdf

local rsync

The rsync command is typically used to copy whole directories. What's great about rsync is that it only copies what has changed in the source directory. So if you regularly rsync a large directory to TACC, it may take a long time the 1st time, but the 2nd time (say after downloading more sequencing data to the source), only the new files will be copied.

rsync is a very complicated program, with many options (http://rsync.samba.org/ftp/rsync/rsync.html). However, if you use it like this for directories, it's hard to go wrong:

rsync -avrP local/path/to/source_directory/ local/path/to/destination_directory/

The -avrP options say "archive mode" (preserve file modification date/time), verbose, recursive and show Progress.

The trailing slash ( / ) on the source and destination directories are very important! rsync will create the last directory level for you, but earlier levels must already exist.

Code Block
language bash title rsync (local directory)
cds rsync -avrP /corral-repl/utexas/BioITeam/web/ucsc_custom_tracks/ data/custom_tracks/

Exercise: What files were copied over?

Expand
title Hint
ls $SCRATCH/data/custom_tracks # or cds; cd data/custom_tracks; ls

Now repeat the rsync and see the difference:

Code Block
language bash
rsync -avrP /corral-repl/utexas/BioITeam/web/ucsc_custom_tracks/ $SCRATCH/data/custom_tracks/

Copy from a remote computer - scp or rsync

Provided that the remote computer is running Linux and you have SSH access to it, you can use various Linux commands to copy data over a secure connection.

The good news is that once you have learned cp and local rsync, remote secure copy (scp) and rsync are very similar!

scp

The scp command copies one or more files from a source to a destination, where either source or destination can be a remote path, of this form:

user_name@host.name:/full/path/to/directory/or/file

or

user_name@host.name:~/path/relative/to/home/directory

Copy a single file your $SCRATCH/data/test1 directory. We don't really need to access corral remotely, of course, but this shows the remote syntax needed. Be sure to change "userid" below to your TACC user id!

Code Block
title cp - single file copy
scp userid@stampede.tacc.utexas.edu:/corral-repl/utexas/BioITeam/web/README.txt $SCRATCH/data/ ls $SCRATCH/data/test1

Notes:

• The 1st time you access a new host the SSH security prompt will appear
• You will always be prompted for your remote host password

The  -r recursive argument works for scp also.

remote rsync

rsync can be run just like before, but using the remote-host syntax. Here we use two tricks:

• The tilde ("~") at the start of the path means "relative to my home directory"
• We traverse through the BioITeam symbolic link created in your home directory earlier (more on this later)

Don't forget to change "userid".

Code Block
language bash title rsync (remote directory)
rsync -avrP userid@stampede.tacc.utexas.edu:~/BioITeam/web/ucsc_custom_tracks/ $SCRATCH/data/custom_tracks/

Exercise: Was anything copied?

Expand
title Answer
No, because all the source files were already present in the destination directory (you copied them earlier) with the same date and times. So rsync had nothing to do!

scavenger hunt exercise

Here's a fun scavenger hunt for more practice. Issue the following commands to get practice what you've learned so far:

Expand
title Hint
Hit Tab Tab as much as possible to save typing!

Code Block
title Play a scavenger hunt for more practice
cd cp -r /corral-repl/utexas/BioITeam/linuxpractice . cd linuxpractice cd what cat readme

Where are you when you're all done?

Expand
title Answer
stamp:~/linuxpractice/what/starts/here/changes/the/world

 

 

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 "$__PERSONAL_PATH__" ]; then export __PERSONAL_PATH__=1 export PATH=.:$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

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 # 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

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 the ~/local/bin directory 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)

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

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