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cd 
ln -s -f $SCRATCH scratch # makes your Home directory the "current directory"
ln -s -f $WORK2$SCRATCH work2scratch
ln -s -f /work2/projects/BioITeam $WORK work
ln -s -f /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools CoreNGS

The tilde character ( ~ ) is a pathname shortcut that means "home Home directory". We'll see more of it later.

$HOME is an environment variable set by TACC that also refers to your home Home area directory.

exit

#!/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#!/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. However, a script inherits the environment variables
# from its parent shell. Both of these are standard bash behavior.
#   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
# There are 3 independent, safe ways to modify the standard module setup:
#   1) Use "module save"  (see "module help" for details).
#   2) Place module commands in ~/.modules
#   3) Place module commands in this file inside the if block below.
if [ -z "$__BASHRC_SOURCED__" -a "$ENVIRONMENT" != BATCH ]; then
  export __BASHRC_SOURCED__=1
  module load launcher
  module load git
fi
############
# SECTION 2 -- environment variables
if [ -z "$__PERSONALBASHRC_PATHSOURCED__" ]; then
  export __PERSONAL_PATH__=1
  # for NGS course
  export LANG="C"  # avoid the annoying Perl warnings on cds, etc. -a "$ENVIRONMENT" != BATCH ]; then
  export PATH=.:$HOME/local/bin:$PATH__BASHRC_SOURCED__=1
  export ALLOCATION=UT-2015-05-18    # Group is G-816696
  export BIWORK=/work2/projects/BioITeam
  export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools
  export BI=/corral-repl/utexas/BioITeammodule load launcher
fi
############
# SECTION 2 -- environment variables
if [ -z "$__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=$LS_COLORS:'di=1;33:fi=01:ln=01;36:'
# For better colors using a darkwhite background terminal, un-comment this line:
##export  export LS_COLORS=$LS_COLORS:'di=1;3334:fi=01:ln=01;36:'
export BIWORK=/work/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools
export BI=/corral-repl/utexas/BioITeam
export ALLOCATION=OTH21164        # For ls6  For better colors using a white backgroundGroup terminal,is unG-comment this line:
#  export LS_COLORS=$LS_COLORS:'di=1;34:fi=01:ln=01;36:'
fi
########################824651
##export ALLOCATION=UT-2015-05-18 # For stampede2  Group is G-816696

##########
# SECTION 3 -- controlling the prompt
if [ -n "$PS1" ]; then PS1='stamp2ls6:\w$ '; fi
##################################
# SECTION 4 -- Umask and aliases and umask
#alias ls="ls --color=always"
alias ll='"ls -la'"
alias lah="ls -lah"
alias lc="wc -l"
alias lhhexdump='lsod -A x -t x1z -lhv'
umask 002
#############################################
# Optional Startup Script tracking
if [ -n "$SHELL_STARTUP_DEBUG" ]; then DBG_ECHO "${DBG_INDENT}}"; fi