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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.

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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 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, perform the steps below:

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

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

cd
cp /workcorral-repl/projectsutexas/BioITeam/projects/courses/Core_NGS_Tools/tacc/core_ngs_tools/login/bashrc.corengs.ls6.dark_bg  ~/.bashrc
chmod 600 ~/.bashrc

Since your ~/.bashrc is executed when you login, to ensure it is set up properly you should first log off ls6 like this:

exit

Then log back in to ls6.tacc.utexas.edu. This time your ~/.bashrc will be executed and you should see a new shell prompt:

ls6:~$

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

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 to your home directory 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:

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 ( ~ ).

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

Since your ~/.bashrc is executed when you login, to ensure it is set up properly you should first log off ls6 like this:

cd
ls -a

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

ls -la

exit

Your Terminal  has logged off of Lonestar6 and is now 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:

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):You should see a new command line prompt:

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.

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 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_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.

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):

cd  
cat .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 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;3433:fi=01:ln=01;36:'
export LANG="C"  # avoid # 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

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

the "she-bang"

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

#!/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.a lot of stuff here; let's look at just a few things.

environment variables

The login script sets several environment variables.

export BIWORK=/work/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools
export ALLOCATION=OTH21164

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). Read more about environment variables here: More on environment variables.

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

export BIWORK=/work/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Toolsecho $CORENGS
echo $ALLOCATION

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 of $BIWORK is the pathname /work/projects/BioITeam). Read more about environment variables here: More on environment variables.

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Follow along with this:

# hit Tab once to expand the environment variable name
ls $BIW 

# hit Tab once after typing $BIWORK/ 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 hit Tab once
# the shell expands as far as it can unambiguously,
# so 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

# now hit Tab twice
# You should see 3 filenames, all starting with "small"
# small.bam  small.fq 
 small2.fq

# 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

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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 – (we'll create that directory shortly), along with a special dot character ( . ) that means "here", or "whatever the current directory is". In the statement below, colon ( : ) separates directories in the list.

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

Create some symbolic links and directories

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

Create some symbolic links and directories

Create some symbolic links that will come in handy later:

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(more on these file system areas soon).

ls -l

ls -l

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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:

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

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