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Old 07-07-2015, 07:05 AM   #1
cmccabe
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Default add to path [solved]

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 at 08:56 AM.
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Old 07-07-2015, 07:38 AM   #2
GenoMax
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Default

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.
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Old 07-07-2015, 08:33 AM   #3
cmccabe
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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 at 08:36 AM.
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Old 07-07-2015, 08:39 AM   #4
GenoMax
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Modify $PATH to include "/home/dnascopev/Desktop/bedops-2.4.14/bin/" and you should be good to go.
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Old 07-07-2015, 08:55 AM   #5
cmccabe
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That was it... thank you .
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Old 07-08-2015, 01:05 PM   #6
cmccabe
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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 .
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