add to path

[cmccabe]

I know this is a basic question, but one I seem to struggle with. After I install and application (bedops) - /home/dnascopev/Desktop/bedops-2.4.14

I add the bin to path or the directory? That is:

path to directory

 export PATH=$PATH:"/media/C2F8EFBFF8EFAFB9/bedops-2.4.14"

path to bin (where all the binaries are)

 export PATH=$PATH:"/media/C2F8EFBFF8EFAFB9/bedops-2.4.14/bin"

At one point it was working but now I get:

dnascopev@ubuntu:~/Desktop/bedops-2.4.14$ bedmap --echo --echo-map-id-uniq epilepsy70_medex_edit.bed gencode.exons.bed > answer.bed
bedmap: command not found

Thank you .

[GenoMax]

Does

$ echo $PATH

include both /media/C2F8EFBFF8EFAFB9/bedops-2.4.14/bin and /home/dnascopev/Desktop/bedops-2.4.14/bin?

What does

$ which bedmap
$ locate bedmap

produce?

BTW: It is not a good idea to make identical copies of folders like this in multiple locations.

[cmccabe]

dnascopev@ubuntu:~/Desktop/bedops-2.4.14$ echo $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:/media/C2F8EFBFF8EFAFB9/bedops-2.14.2/bin:/media/C2F8EFBFF8EFAFB9/bedops-2.4.14/bin:/media/C2F8EFBFF8EFAFB9/bedops-2.4.14

dnascopev@ubuntu:~/Desktop/bedops-2.4.14$ which bedmap

dnascopev@ubuntu:~/Desktop/bedops-2.4.14$ locate bedmap
/home/dnascopev/Desktop/bedops-2.4.14/bin/bedmap

I moved bedops off the media device because I thought that maybe that would help solve the permission denied error was getting. Thank you .

[GenoMax]

Modify $PATH to include "/home/dnascopev/Desktop/bedops-2.4.14/bin/" and you should be good to go.

[cmccabe]

That was it... thank you .

[cmccabe]

would the below permanently add the path?

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

whenever I close the terminal path keeps reseting so I am hoping this solves it. Thank you .