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#!/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:$PATH
  export PYTHONPATH=$BIWORK/ls5/lib/python2.7/site-packages:$PYTHONPATH

  # for Turn on coloring by file type in the shell
  export LS_OPTIONS='-N --color=auto -T 0'
  # For better colors using a blackwhite background terminal, un-comment this line:
  #export LS_COLORS=$LS_COLORS:'di=1;33:'  
  # forFor better colors using a white background terminal, un-comment this line:
  #export LS_COLORS=$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