install_help/example_bash_profile at master · jbadomics/install_help · GitHub

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shopt -s checkwinsize
eval $(resize > /dev/null 2>&1)

# reset PATH to default
PATH=$(getconf PATH)

# add paths to executables
PATH=.:$PATH
PATH=/usr/local/bin:$PATH
PATH=/usr/local/bin/bin:$PATH
PATH=/usr/local/sbin:$PATH
PATH=/sw:$PATH
PATH=/sw/scripts:$PATH
PATH=/sw/signalp-4.1:$PATH
PATH=~/Documents/Bond/Bioinformatics/scripts:$PATH
PATH=/sw/breseq-0.27.1-MacOSX-10.7+/bin:$PATH
PATH=/sw/get_homologues-macosx-20150814:$PATH
PATH=/sw/phylosift_v1.0.1:$PATH
PATH=/sw/idba-1.1.2/bin:$PATH
PATH=/sw/pullseq/bin:$PATH
PATH=/sw/circos-0.69/bin:$PATH
PATH=/sw/sumaclust_v1.0.10:$PATH
PATH=/sw/ssaha2_v2.5.5_x86_64:$PATH
PATH=/sw/bbmap:$PATH
PATH=/sw/mothur:$PATH

export PATH="$(brew --prefix coreutils)/libexec/gnubin:$PATH"

set -o noclobber # prevents existing files from being overwritten

# export MANPATH=/usr/local/opt/coreutils/libexec/gnuman
alias man='_() { echo $1; man -M $(brew --prefix)/opt/coreutils/libexec/gnuman $1 1>/dev/null 2>&1;  if [ "$?" -eq 0 ]; then man -M $(brew --prefix)/opt/coreutils/libexec/gnuman $1; else man $1; fi }; _'

alias find='gfind'
alias locate='glocate'
alias oldfind='goldfind'
alias updatedb='gupdatedb'
alias xargs='gxargs'
alias ls='ls --color'
alias vpn='open -a /Applications/Cisco/Cisco\ AnyConnect\ Secure\ Mobility\ Client.app/'
alias ff='open -a /Applications/Firefox.app/'
alias fz='open -a /Applications/FileZilla.app/'
alias bu='brew update'
alias bd='brew doctor'
alias bc='brew cleanup --force'
alias bp='brew prune'
alias upgrade='for keg in $(brew list); do brew upgrade $keg; done'
alias update='brew update && brew cleanup --force && brew prune && brew doctor'
alias grep='grep --color=auto'
alias rc='source ~/.bash_profile'
alias edit='open -a /Applications/TextEdit.app/'
alias tw='open -a /Applications/TextWrangler.app/'
alias preview='open -a /Applications/Preview.app/'
alias gepard='java -Xmx2g -jar /sw/gepard-1.30/gepard.jar &'
alias esom='/sw/ESOM/bin/esomana &'
alias perlpath='perl -e "print \"@INC\"" | tr " " "\n" | sort'
alias perlmodules='~/.listmodules.pl 2> /dev/null'
alias pythonmodules='pip freeze'
alias printpath='/bin/echo $PATH | tr ":" "\n"'
alias sortpath='printpath | sort -f 2> /dev/null'
alias show='defaults write com.apple.finder AppleShowAllFiles YES; killall Finder /System/Library/CoreServices/Finder.app'
alias hide='defaults write com.apple.finder AppleShowAllFiles NO; killall Finder /System/Library/CoreServices/Finder.app'
alias openwith='/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -r -domain local -domain user;killall Finder;echo "Open With has been rebuilt, Finder will relaunch"'

function gcc_on {
	export CC=$(which gcc-6)
	export CXX=$(which g++-6)
	export CPP=$(which cpp-6)
	export LD=$(which gcc-6)
	alias c++='echo $(which c++-6)'
	alias g++='echo $(which g++-6)'
	alias gcc='echo $(which gcc-6)'
	alias cpp='echo $(which cpp-6)'
	alias ld='echo $(which gcc-6)'
	alias cc='echo $(which gcc-6)'

	gcc_version=$(gcc-6 --version | head -n 1)
	gcc_path=$(brew info gcc | grep '/usr' | sed 's/ .*/\/bin/')
	echo "now using Homebrew-installed GNU $gcc_version at $gcc_path"
	echo "setting build flags and aliases"
	echo "CC=$CC"
	echo "CXX=$CXX"
	echo "CPP=$CPP"
	echo "LD=$LD"
	echo "NOTE: these paths are symlinked to $gcc_path by Homebrew"
}

function gcc_off {
	unset CC
	unset CXX
	unset CPP
	unset LD
	unalias c++ >/dev/null 2>&1
	unalias g++ >/dev/null 2>&1
	unalias gcc >/dev/null 2>&1
	unalias cpp >/dev/null 2>&1
	unalias ld >/dev/null 2>&1
	unalias cc >/dev/null 2>&1

	echo "unsetting build flags and aliases for GNU gcc"
	echo "now using $(gcc --version 2> /dev/null | grep Apple) at $(which gcc)"
}