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permission denied error

I added bedops-2.14.2 to path using:

export PATH=$PATH:"/media/C2F8EFBFF8EFAFB9/bedops-2.14.2"

and am trying to run:

dnascopev@ubuntu:/media/C2F8EFBFF8EFAFB9$ gunzip --stdout gencode.v21.annotation.gtf.gz \
>     | gtf2bed - \
>     | grep "exon" \
>     > gencode.exons.bed
bash: /media/C2F8EFBFF8EFAFB9/bedops-2.14.2/bin/gtf2bed: Permission denied

I can not figure out why I am getting the error? Thank you :).

bedops
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updated by Ram Ram • written by bioguy24 bioguy24

gtf2bed is not executable, not really a bioinformatics question, but chmod +x might help you

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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

Hello cmccabe!

We believe that this post does not fit the main topic of this site.

Please Google. Ask stackoverflow if you must.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by Ram Ram

Thank you and I apologize :).

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written by bioguy24 bioguy24

add this in .bashrc file export PATH=$PATH:"/media/C2F8EFBFF8EFAFB9/bedops-2.14.2/"

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written by DareDevil DareDevil

1 answer

It looks like the file isn't set as an executable or you lack privileges for that directory.

sudo chmod +x /media/C2F8EFBFF8EFAFB9/bedops-2.14.2/bin/gtf2bed

If that doesn't work, try moving the executable off of the media device and into a new directory such as /usr/local/bin

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updated by Ram Ram • written by muppetleague • muppetleague

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