add to path doesn't stay

[cmccabe]

I am using the below command to add to path:

 export PATH=$PATH:"/home/dnascopev/Desktop/bedops-2.4.14/bin/" >> ~/.bashrc

However, the path does not stay or add and resets as soon as I close. Is there something wrong with my command? Thanks .

[GenoMax]

You need to do

$ echo export PATH=$PATH:"/home/dnascopev/Desktop/bedops-2.4.14/bin/" >> ~/.bashrc

Then it should get added to the end of that file. Verify it afterwards

$ cat ~/.bashrc

[fanli]

You probably meant to add that line to your .bashrc instead of running it at the shell prompt

So:

echo "export PATH=$PATH:"/home/dnascopev/Desktop/bedops-2.4.14/bin/"" >> ~/.bashrc

[cmccabe]

I tried that command and here is the output and the bedops error, path appers to be added? Thank you .

dnascopev@ubuntu:~$ echo export PATH=$PATH:"/home/dnascopev/Desktop/bedops-2.4.14/bin/" >> ~/.bashrc
dnascopev@ubuntu:~$ cat ~/.bashrc
# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples

# If not running interactively, don't do anything
[ -z "$PS1" ] && return

# don't put duplicate lines or lines starting with space in the history.
# See bash(1) for more options
HISTCONTROL=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 [ -f /etc/bash_completion ] && ! shopt -oq posix; then
    . /etc/bash_completion
fi
export PATH=$PATH:/home/dnascopev/Desktop/bedtools2-2.20.1
export PATH=/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/dnascopev/Desktop/bedtools2-2.20.1:/home/dnascopev/Desktop/bedops-2.4.14/bin/
dnascopev@ubuntu:~$ cd "/home/dnascopev/Desktop/bedops-2.4.14"
dnascopev@ubuntu:~/Desktop/bedops-2.4.14$ sort -k1,1 -k2,2g -o sort_3column_xgen_targets.bed 3column_xgen_targets.bed
dnascopev@ubuntu:~/Desktop/bedops-2.4.14$ bedmap --echo --skip-unmapped --delim '\t' --echo-map-id-uniq sort_3column_xgen_targets.bed sort_gene.bed > answer.bed 
bedmap: command not found

[GenoMax]

Is bedmap in "/home/dnascopev/Desktop/bedops-2.4.14/bin/" directory?

It may need to have the execute bit set,

$ chmod a+x /home/dnascopev/Desktop/bedops-2.4.14/bin/bedmap

[cmccabe]

I tried:

 
echo "export PATH=$PATH:"/home/dnascopev/Desktop/bedops-2.4.14/bin/"" >> ~/.bashrc

and

echo "export PATH=$PATH:"chmod a+x /home/dnascopev/Desktop/bedops-2.4.14/bin/"" >> ~/.bashrc

and got the same error as above.

bedmap is in the home/dnascopev/Desktop/bedops-2.4.14/bin/ directory.

If I use:

export PATH=$PATH:"/home/dnascopev/Desktop/bedops-2.4.14/bin/" >> ~/.bashrc

tthe path is added but then resets after I exit. Thank you .

[GenoMax]

echo "export PATH=$PATH:"chmod a+x /home/dnascopev/Desktop/bedops-2.4.14/bin/"" >> ~/.bashrc

and got the same error as above.

bedmap is in the home/dnascopev/Desktop/bedops-2.4.14/bin/ directory.

That chmod command was not for inclusion in the .bashrc file. You were supposed to run it in terminal.

What do you get with the following commands?

$ which bedmap
$ bedmap --help

Before you do any additional damage spend the remaining day at this link brushing up on unix basics: http://korflab.ucdavis.edu/Unix_and_...ent.html#part1

[cmccabe]

Thank you for the link, I appreciate it