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The Terminal window

• Macs and Linux have a Terminal programs program built-in – find it now on your computerWindows needs helpPutty – 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
• 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
    

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• terminal plus minimal Linux environment
  • has ssh, scp but not rsync

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• a full Linux environment, including X-windows for running GUI programs remotely
• really the best, but complicated to install

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SSH

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 Lonestar5 Lonestar6 compute cluster at TACC (Texas Advanced Computing Center), where the remote host name is ls5ls6.tacc.utexas.edu.

On Macs, Linux and Windows (Git-bash or Cygwin), you run ssh from a Terminal window.

In your local Terminal window:

ssh your<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

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  PuTTY as your Terminal from Windows: Double-click the Putty

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  icon In the PuTTY Configuration window make sure the Connection type is SSH enter

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  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

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  provide your 2-factor authentication code

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  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 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

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

  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
  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.

  ...

  
  

  $WORK and $SCRATCH are TACC environment variable that refer to your work and scratch file system areas. To see the value of an environment variable, use the echo command

  Warning
  If you already have a .bashrc set up, make a backup copy first. cd Code Block language bash
  title	Create symbolic directory links
  cd ls -la ln # -s Do -f you $SCRATCH see scratch ln -s -f $WORK work ln -s -f /work/projects/BioITeam
  Tip
  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:

  expand

  Code Block
  language bash
  echo $SCRATCH
  title What is ln 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 $HOME/local/bin directory and link a scripts there that we will use a lot in the class.

  Code Block
  language bash title Set up $HOME/local/bin directory
  mkdir -p ~/local/bin cd ~/local/bin ln -s -f /work/projects/BioITeam/common/bin/launcher_creator.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.

  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 /work/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.ls5 .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 ls5 like this:

  Code Block
  language bash title Log off Lonestar5
  exit

  Then log back in to ls5.tacc.utexas.edu. This time your .bashrc will be executed and you should see a new shell prompt:

  Code Block
  ls5:~$

  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: ls5:~/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

  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 echos 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):

  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 # for NGS course module load python module load launcher fi ########## # SECTION 2 -- environment variables if [ -z "$__PERSONAL_PATH__" ]; then export __PERSONAL_PATH__=1 # for NGS course export ALLOCATION=UT-2015-05-18 export BIWORK=/work/projects/BioITeam export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools export PATH=.:$HOME/local/bin:$PATH export PYTHONPATH=$BIWORK/ls5/lib/python2.7/site-packages:$PYTHONPATH # for better colors using a black background terminal: #export LS_COLORS=$LS_COLORS:'di=1;33:' # for better colors using a white background terminal: #export LS_COLORS=$LS_COLORS:'di=1;34:' fi ########## # SECTION 3 -- controlling the prompt # for NGS course if [ -n "$PS1" ]; then PS1='ls5:\w$ ' fi ########## # SECTION 4 -- Umask and aliases # for NGS course umask 002 alias ll="ls -la" alias lah="ls -lah" ########## # 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. 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
  language bash title The "she-bang" line
  #!/bin/bash

  environment variables

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

  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 a programming language 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).

  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 /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

  Code Block
  language bash title Shell completion exercise
  # hit Tab once after typing $BIWORK/ 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 "m" and one Tab ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/m # your command line should now look like this ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/ # now hit Tab once # the shell expands as far as it can unambiguously, # so your command line should look like this ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small # now hit Tab twice # You should see 3 filenames, all starting with "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 # 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 shortly.

  Here's how the common login script adds your $HOME/local/bin directory to the location list – recall that's where we a script 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
  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 # for NGS course if [ -n "$PS1" ]; then PS1='ls5:\w$ ' fi

  File systems at TACC

  The first thing you'll want to do is transfer your sequencing data to TACC so you can process it there. Here is an overview of the different storage areas at TACC, their characteristics, and Linux commands generally used to perform the data transfers:

  • wget – retrieves the contents of an Internet URL
  • cp – copies files located on any local file system
  • scp – copies files to/from a remote system
  • rsync – copies files on either local or remote systems

  ...

  Image Removed

  Local file systems

  There are 3 local file systems available on any TACC compute cluster (Lonestar5, stampede2, etc.), each with different characteristics. All these local file systems are very fast and set up for parallel I/O (Lustre file system).

  On l5 these local file systems have the following characteristics:

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  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 4856 2018-09-30 | A-cm10 1096 2018-12-31 | | UT-2015-05-18 2100 2019-03-31 | genomeAnalysis 2500 2019-03-31 | ------------------------ Disk quotas for user abattenh ------------------------- | Disk Usage (GB) Limit %Used File Usage Limit %Used | | /home1 0.0 10.0 0.12 91 1000000 0.01 | | /work 538.5 1024.0 52.59 61053 3000000 2.04 | | /scratch 3725.9 0.0 0.00 4137 0 0.00 | -------------------------------------------------------------------------------

  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 title Changing file systems at TACC
  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.

  Stockyard (shared Work)

  TACC compute clusters now share a common Work file system called stockyard. So files in your Work area do not have to be copied, for example from ls5 to stampede2 – they can be accessed directly from either cluster.

  Note that there are two environment variables pertaining to the shared Work area:

  • $STOCKYARD - This refers to the root of your shared Work area
    • e.g. /work/01063/abattenh
  • $WORK - Refers to a sub-directory of the shared Work area that is different for different clusters, e.g.:
    
    • /work/01063/abattenh/lonestar on ls5
    • /work/01063/abattenh/stampede2 on stampede2

  A mechanism for purchasing larger stockyard allocations (above the 1 TB basic quota) are in development.

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

  Code Block
  language bash title The shared BioITeam directory
  ls /work/projects/BioITeam

  Files we will use in this course are in a sub-directory there:

  Code Block
  language bash title Our shared class directory
  ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools

  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 ~$85/TB/year.

  The UT/Austin BioInformatics Team also has an older, common directory area on corral.

  Code Block
  language bash title The legacy BioITeam directory on Corral
  ls /corral-repl/utexas/BioITeam

  A couple of things to keep in mind regarding corral:

  • corral is a great place to store data in between analyses.
    • Store your permanent, original sequence data on corral
    • Copy the data you want to work with from corral to $SCRATCH
    • Run your analyses (batch jobs)
    • Copy your results back 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 ls5 clusters. So remote copy commands are needed to copy data to and from ranch (e.g. scp, rsync).

  Staging your data

  So, your sequencing center has some data for you. They may send you a list of web or FTP links to use to download the data.

  The first task is to get this sequencing 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 title Create a pretend "archive" directory
  mkdir -p $WORK/archive/original/2018_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)
    • sub-directories named by year_month.<project_name>
  • aligned – for alignment artifacts (bam files, etc)
    • sub-directories named by year_month.<project_name>
  • analysis – further downstream analysis
    • reasonably named subdirectories, often by project
  • genome – reference genomes and other annotation files used in alignment and analysis
    
    • sub-directories 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 title Get ready to wget
  cd $WORK/archive/original/2018_05.core_ngs 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 (Windows) or Control+click (Mac) 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 (Windows), or Paste (Command-V on Mac, Control-V on Windows). The command line to be executed should now look like this:

  Code Block
  language bash title wget to retrieve a web URL
  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. Check that you now see the two files (ls).

  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 Single file copy with cp
  mkdir -p $SCRATCH/data/test1 cp /corral-repl/utexas/BioinformaticsResource/web/CoreNGS/README.txt $SCRATCH/data/test1/ ls $SCRATCH/data/test1 # or.. ls ~/scratch/data/test1 # or.. cd $SCRATCH/data/test1 ls

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

  Code Block
  language bash title Directory copy with cp
  cds cd data cp -r /corral-repl/utexas/BioinformaticsResource/web/CoreNGS/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

  ...

  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

  (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 this:

  Code Block
  language bash 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 # 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 "$__PERSONAL_PATH__" ]; then export __PERSONAL_PATH__=1 export PATH=.:$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

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

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

  Both the source and target directories are local (in some file system accessible directly from ls5). Either full or relative path syntax can be used for both.

  The -avrP options say "archive mode" (preserve file modification date/time), verbose, recursive and show Progress. Since these are all single-character options, they can be combined after one option prefix dash ( - ).

  Tip
  title Always add a trailing slash ( / ) after directory names
  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/BioinformaticsResource/web/CoreNGS/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.

  Use the up-arrow to retrieve the previous command from your bash command history.

  Code Block
  language bash
  rsync -avrP /corral-repl/utexas/BioinformaticsResource/web/CoreNGS/ucsc_custom_tracks/ data/custom_tracks/

  Tip
  The bash shell has several convenient line editing features: use the up arrow to scroll back through the command line history; down arrow goes forward use Ctrl-a to move the cursor to the beginning of a line; Ctrl-e to the end use Backspace to remove text before the cursor; Delete to remove text after the cursor

  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 remote rsync are very similar!

  scp

  The scp command copies one or more files from a source to a destination, where either source or destination, or both, can be a remote path.

  Remote paths are similar to local paths, but have user and host information first:

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

  -- or –

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

  Copy a single file to 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 single remote file copy with scp
  scp userid@stampede.tacc.utexas.edu:/corral-repl/utexas/BioITeam/web/README.txt $SCRATCH/data/test1 ls $SCRATCH/data/test1

  Notes:

  • The 1st time you access a new host the SSH security prompt will appear
  • You will normally be prompted for your remote host password
    • that step is skipped here because you're really not accessing a remote host
  • The  -r recursive argument works for scp also, just like for cp

  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.
  • We use the same tilde ( ~ ) in the destination to traverse the scratch symbolic link in your home directory.

  Don't forget to change userid below.

  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!

  To get started:

  Code Block
  title Play a scavenger hunt for more practice
  cd cp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/what what cd what cat readme

  Where are you when you're all done?

  Expand
  title Answer
  ls5:~/what/starts/here/changes/the/world