Getting started at TACC

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 putty.exe (terminal) and pscp.exe (secure copy client)
  • Git for Windows with bash – https://git-for-windows.github.io/   
    
    • terminal plus minimal Linux environment
      • has ssh, scp but not rsync
  • Cygwin – http://www.cygwin.com/
    
    • a full Linux environment, including X-windows for running GUI programs remotely
    • really the best, but complicated to install
  • Windows 10 Pro – includes a Ubuntu-like bash shell
    • see https://msdn.microsoft.com/en-us/commandline/wsl/about

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 compute cluster at TACC, where the remote host name is ls5.tacc.utexas.edu.

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

ssh your_TACC_userID@ls5.tacc.utexas.edu

• Answer yes to the SSH security question prompt
• Enter the password associated with your TACC account
• Wait for your 2-factor authentication code to arrive via SMS or app, then type it in

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

• Double-click the Putty.exe icon
• In the PuTTY Configuration window
  • make sure the Connection type is SSH
  • enter ls5.tacc.utexas.edu for Host Name
  • 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
  • wait for your 2-factor authentication code to arrive via SMS or app, then type it in

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 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.

Setting up your environment

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

Create some symbolic links that will come in handy later:

cd 
ln -s -f $SCRATCH scratch
ln -s -f $WORK work
ln -s -f /work/projects/BioITeam

echo $SCRATCH

ls -l

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

mkdir -p ~/local/bin
cd ~/local/bin
ln -s -f /work/projects/BioITeam/common/bin/launcher_maker.py
ln -s -f /work/projects/BioITeam/ls5/opt/cutadapt-1.10/bin/cutadapt
ln -s -f /work/projects/BioITeam/ls5/opt/multiqc-1.0/multiqc
ln -s -f /work/projects/BioITeam/ls5/opt/samstat-1.09/samstat

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:

cd
cp .bashrc .bashrc.beforeNGS

cd
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.ls5  .bashrc
chmod 600 .bashrc

Since .bashrc is executed when you login, to ensure it is set up properly you should first log off ls5 like this:

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:

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.

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:

cd
ls -a

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

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):

cd
cat .bashrc

# or for larger files...
more .bashrc

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

#!/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 python
  module load launcher
fi
############
# SECTION 2 -- environment variables
if [ -z "$__PERSONAL_PATH__" ]; then
  export __PERSONAL_PATH__=1

# For CCBB summer school courses
  export ALLOCATION=UT-2015-05-18
  export BI=/corral-repl/utexas/BioITeam
  export BIWORK=/work/projects/BioITeam
  export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools
  export PATH=.:$HOME/local/bin:$PATH
  # For cutadapt support:
  export PYTHONPATH=$BIWORK/ls5/lib/python2.7/site-packages:$PYTHONPATH
  # For MultiQC support:
  export PYTHONPATH=$BIWORK/ls5/lib/python2.7/annab-packages:$PYTHONPATH

# Turn on coloring by file type in the shell
  export LS_OPTIONS='-N --color=auto -T 0'
  # For better colors using a white background terminal, un-comment this line:
  #export LS_COLORS=$LS_COLORS:'di=1;33:'
  # For better colors using a white background terminal, un-comment this line:
  #export LS_COLORS=$LS_COLORS:'di=1;34:'
fi
##########
# SECTION 3 -- controlling the prompt
if [ -n "$PS1" ]; then
  PS1='ls5:\w$ '
fi
##########
# SECTION 4 -- Umask and aliases
umask 002
alias ll="ls -la"
alias lah="ls -lah"
alias hexdump='od -A x -t x1z -v'
##########
# 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).

#!/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.

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.

# 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:

echo $PATH

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

Here's how the common login script adds your $HOME/local/bin directory to the location list – 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 below, colon ( : ) separates directories in the list.

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".

##########
# 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

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 ls5 these local file systems have the following characteristics:

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

--------------------- 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 file systems

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.

cdw
cds
cd

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.

ls /work/projects/BioITeam

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

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.

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 stampede2 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.

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.

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:

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.

mkdir -p $SCRATCH/data/test1
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small.fq  $SCRATCH/data/test1/
ls $SCRATCH/data/test1

# or..
mkdir -p ~/scratch/data/test1
cd ~/scratch/data/test1
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small.fq  .
ls

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

cds
cd data
cp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools/general/ general/

Exercise: What files were copied over?

ls general

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 the recipe shown here for directories, it's hard to go wrong:

rsync -ptlrvP 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 -ptlrvP options above stand for:

• -p means preserve file permissions
• -t means preserve file times
• -l means copy symbolic links as links
• -r means recursively copy sub-directories
• -v means verbose
• -P means show Progress.

Since these are all single-character options, they can be combined after one option prefix dash ( - ). You could also use options -arvP, where -a means "archive mode", which implies the -ptl options.

cds
rsync -ptlrvP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/ucsc_custom_tracks/ data/custom_tracks/

Exercise: What files were copied over?

ls $SCRATCH/data/custom_tracks
# or
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.

rsync -ptlrvP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/ucsc_custom_tracks/ 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 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 from the server named gapdh.icmb.utexas.edu, using the user account corengstools. When prompted for a password, use the one we have written on the board (or copy/paste the password from this file: $CORENGS/tacc/gapdh_access.txt)

cds
cat $CORENGS/tacc/gapdh_access.txt
scp corengstools@gapdh.icmb.utexas.edu:~/custom_tracks/progeria_ctcf.vcf.gz ./data/test1/
ls ./data/test1

Notes:

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

rsync -ptlrvP corengstools@gapdh.icmb.utexas.edu:~/custom_tracks/ ~/scratch/data/custom_tracks/

Exercise: Was anything copied?

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:

To get started:

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?

step by step answers

mkdir starts
cd starts
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/steps/nextInstr .
cat nextInst

mkdir here
cd here
wget http://web.corral.tacc.utexas.edu/BioITeam/step3.txt
cat step3.txt

rsync -ptlrvP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/ changes/
# or
scp -r scp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes changes

# Then
cd changes 
more largeFile.txt

rsync -ptlrvP corengstools@gapdh.icmb.utexas.edu:~/the/ the/
cd the
cat instr5.txt
cd world
cat instr6.txt