#!/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 "$__PERSONAL_PATH__" ]; then
export __PERSONAL_PATH__=1
# Forfor CCBB summer school courses
export PATH=.:$HOME/local/bin:$PATH
export ALLOCATION=UT-2015-05-18
export BI=/corral-repl/utexas/BioITeam
export BIWORK=/work/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools
export PATH=.:$HOME/local/bin:$PATH
# For cutadapt support:BI=/corral-repl/utexas/BioITeam
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 |