#-----------------------------------------------------------+
#
# Jamie's BASH
#
#-----------------------------------------------------------+
#
#  AUTHOR: Jamie Estill
# STARTED: 02/15/2006
# UPDATED: 10/19/2006
#
# User specific aliases and functions
#
#-----------------------------------------------------------+

#-----------------------------+
# MY LOCAL PATHS              |
#-----------------------------+
#export PATH=$PATH:/usr/local/genome/ncbiblast/2.2.9
export PATH=$PATH:/usr/local/genome/ncbiblast/blast-2.2.13/bin
export PATH=$PATH:/usr/local/genome/repeatmasker/RepeatMasker2006Jan20
export PATH=$PATH:/usr/local/genome/dialign/dialign2_dir
export PATH=$PATH:/usr/local/genome/paml/paml3.15/bin
export PATH=$PATH:/usr/local/genome/lucy/lucy-1.19p

# APPS IN MY HOME DIR
export PATH=$PATH:/home/jestill/Apps/Cytoscape-v2.3
export PATH=$PATH:/home/jestill/Apps/Apollo_1.6.5
export PATH=$PATH:/home/jestill/Apps/tgicl_linux
export PATH=$PATH:/home/jestill/Apps/SeqClean/seqclean
export PATH=$PATH:/home/jestill/Apps/clview
export PATH=$PATH:/home/jestill/Apps/
export PATH=$PATH:/home/jestill/Apps/bin/
export PATH=$PATH:/home/jestill/projects/scripts/bin
# ADDED LUCY TO THE /USR/LOCAL/GENOME FOLDER -- 10/02/2006
#export PATH=$PATH:/home/jestill/Apps/lucy/lucy-1.19p

#-----------------------------+
# ENVIRONMENTAL VARIABLES     |
#-----------------------------+
export EDITOR=emacs
# 07/28/2006
# Added the following 5/25/2006 for MySQL ODBC
export ODBCINI=/etc/odbc.ini
export ODBCSYSINI=/etc
#07/28/2006
export DIALIGN2_DIR=/usr/local/genome/dialign/dialign2_dir/

#----------------------------+
# SOURCE GLOBAL DEFINITIONS  |
#----------------------------+
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

#----------------------------+
# COMMAND ALIASES            |
#----------------------------+
alias ls='ls -lhF --color'
alias more='less'

# 5/22/2006
# Using ftp -i alows for mget without interactive
alias ftp='ftp -i'

#5/24/2006
alias du='du -h --max-depth=1'
#10/19/2006
alias lx='ls -lXB'              # sort by extension
alias lk='ls -lSr'              # sort by size
alias lt='ls -ltr'              # sort by date

#-----------------------------+
# FUNCTIONS                   |
#-----------------------------+

# 10/19/2006
function my_ps() { ps $@ -u $USER -o pid,%cpu,%mem,bsdtime,command ; }
function pp() { my_ps f | awk '!/awk/ && $0~var' var=${1:-".*"} ; }