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  • add to path

    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
    Code:
     export PATH=$PATH:"/media/C2F8EFBFF8EFAFB9/bedops-2.4.14"
    path to bin (where all the binaries are)
    Code:
     export PATH=$PATH:"/media/C2F8EFBFF8EFAFB9/bedops-2.4.14/bin"
    At one point it was working but now I get:

    Code:
    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 .
    Last edited by cmccabe; 07-07-2015, 08:56 AM.

  • #2
    Does

    Code:
    $ echo $PATH
    include both /media/C2F8EFBFF8EFAFB9/bedops-2.4.14/bin and /home/dnascopev/Desktop/bedops-2.4.14/bin?

    What does

    Code:
    $ which bedmap
    $ locate bedmap
    produce?

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

    Comment


    • #3
      Code:
      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 .
      Last edited by cmccabe; 07-07-2015, 08:36 AM.

      Comment


      • #4
        Modify $PATH to include "/home/dnascopev/Desktop/bedops-2.4.14/bin/" and you should be good to go.

        Comment


        • #5
          That was it... thank you .

          Comment


          • #6
            would the below permanently add the path?

            Code:
             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 .

            Comment

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