Ubuntu

Command 'lesspipe' is available in the following places
 * /bin/lesspipe
 * /usr/bin/lesspipe
The command could not be located because '/usr/bin:/bin' is not included in the PATH environment variable.
lesspipe: command not found
Command 'dircolors' is available in '/usr/bin/dircolors'
The command could not be located because '/usr/bin' is not included in the PATH environment variable.
dircolors: command not found
Command 'ls' is available in '/bin/ls'
The command could not be located because '/bin' is not included in the PATH environment variable.
ls: command not found

cmccabe@HP-Z640-Workstation:~$ cat ~/.bashrc
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples

# If not running interactively, don't do anything
case $- in
    *i*) ;;
      *) return;;
esac

# don't put duplicate lines or lines starting with space in the history.
# See bash(1) for more options
export PATH=/home/cmccabe/Desktop/ngs_analysis/samtools-1.2:$PATHHISTCONTROL=ignoreboth

# append to the history file, don't overwrite it
shopt -s histappend

# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
HISTSIZE=1000
HISTFILESIZE=2000

# check the window size after each command and, if necessary,
# update the values of LINES and COLUMNS.
shopt -s checkwinsize

# If set, the pattern "**" used in a pathname expansion context will
# match all files and zero or more directories and subdirectories.
#shopt -s globstar

# make less more friendly for non-text input files, see lesspipe(1)
[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"

# set variable identifying the chroot you work in (used in the prompt below)
if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
    debian_chroot=$(cat /etc/debian_chroot)
fi

# set a fancy prompt (non-color, unless we know we "want" color)
case "$TERM" in
    xterm-color) color_prompt=yes;;
esac

# uncomment for a colored prompt, if the terminal has the capability; turned
# off by default to not distract the user: the focus in a terminal window
# should be on the output of commands, not on the prompt
#force_color_prompt=yes

if [ -n "$force_color_prompt" ]; then
    if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
    # We have color support; assume it's compliant with Ecma-48
    # (ISO/IEC-6429). (Lack of such support is extremely rare, and such
    # a case would tend to support setf rather than setaf.)
    color_prompt=yes
    else
    color_prompt=
    fi
fi

if [ "$color_prompt" = yes ]; then
    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
else
    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
fi
unset color_prompt force_color_prompt

# If this is an xterm set the title to user@host:dir
case "$TERM" in
xterm*|rxvt*)
    PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
    ;;
*)
    ;;
esac

# enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
    test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
    alias ls='ls --color=auto'
    #alias dir='dir --color=auto'
    #alias vdir='vdir --color=auto'

    alias grep='grep --color=auto'
    alias fgrep='fgrep --color=auto'
    alias egrep='egrep --color=auto'
fi

# some more ls aliases
alias ll='ls -alF'
alias la='ls -A'
alias l='ls -CF'

# Add an "alert" alias for long running commands.  Use like so:
#   sleep 10; alert
alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'

# Alias definitions.
# You may want to put all your additions into a separate file like
# ~/.bash_aliases, instead of adding them here directly.
# See /usr/share/doc/bash-doc/examples in the bash-doc package.

if [ -f ~/.bash_aliases ]; then
    . ~/.bash_aliases
fi

# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
  if [ -f /usr/share/bash-completion/bash_completion ]; then
    . /usr/share/bash-completion/bash_completion
  elif [ -f /etc/bash_completion ]; then
    . /etc/bash_completion
  fi
fi
export PATH=$PATH:export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
export PATH=$PATH:export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
export PATH=$PATH:/home/cmccabe/tabix-0.2.6

# export PATH=$PATH:export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin$
# export PATH=$PATH:export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin$
#export PATH=$PATH:/home/cmccabe/tabix-0.2.6

# [ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"
# if [ -x /usr/bin/dircolors ]; then

Command 'lesspipe' is available in the following places
 * /bin/lesspipe
 * /usr/bin/lesspipe
The command could not be located because '/usr/bin:/bin' is not included in the PATH environment variable.
lesspipe: command not found
Command 'dircolors' is available in '/usr/bin/dircolors'
The command could not be located because '/usr/bin' is not included in the PATH environment variable.
dircolors: command not found
Command 'ls' is available in '/bin/ls'
The command could not be located because '/bin' is not included in the PATH environment variable.
ls: command not found
cmccabe@HP-Z640-Workstation:~$ nano .bashrc
Command 'nano' is available in the following places
 * /bin/nano
 * /usr/bin/nano
The command could not be located because '/bin:/usr/bin' is not included in the PATH environment variable.
nano: command not found