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If your Windows version does not have ssh in Command Prompt or PowerShell:

• Download the free PuTTY suite of remote access tools, which includes a nice Terminal program: https://www.chiark.greenend.org.uk/~sgtatham/putty/

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

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

If you're using

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

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.

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

mkdir -p $HOME/local/bin
cd $HOME/local/bin
ln -s -f/core_ngs_tools/login/bashrc.corengs.ls6.dark_bg  ~/.bashrc
chmod 600 ~/.bashrc

cp /corral-repl/utexas/BioITeam/bin/launcher_creator.py

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

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.

exit

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

ls6:~$

# 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$ 

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

$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)

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.

ls -l

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

cd

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

cd  
cat .bashrc

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.

#!/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

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

echo $CORENGS

ls $CORENGS

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

# 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

echo $PATH

cat .profile_user

#!/bin/bash
# Change the command line prompt to contain the current directory name
PS1='stamp:\w$ '

# Ensure all created files can be read/written by group members
umask 002

# Use yellow for directories, not that horrible blue
dircolors .dircolors > /dev/null

# Make common useful software available
module load python
module load launcher

# 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

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