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  • cmccabe
    Senior Member
    • Jul 2012
    • 355

    #1

    permisson denied error in bedops-2.14.4

    Seems to be added to path, but I am getting the below error. What is wrong? Thank you .

    Code:
    cmccabe@HPZ640:~$ echo $PATH
    /home/cmccabe/Desktop/NGS/bedops-2.14.4/bin:/home/cmccabe/Desktop/NGS/samtools-1.2:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
    cmccabe@HPZ640:~$ cd "/home/cmccabe/Desktop/NGS"
    cmccabe@HPZ640:~/Desktop/NGS$ gunzip --stdout /home/cmccabe/Desktop/bed/gencode.v19.annotation.gtf.gz \
    >     | gtf2bed - \
    >     | grep "exon" \
    >     > /home/cmccabe/Desktop/NGS/bed/gencode.exons.bed
    [B]bash: /home/cmccabe/Desktop/NGS/bedops-2.14.4/bin/gtf2bed: Permission denied[/B]

    EDIT: tried chmod as well
    Code:
     chmod +x /home/cmccabe/Desktop/NGS/bedops-2.14.4/bin*
    Last edited by cmccabe; 09-16-2015, 01:30 PM. Reason: added edit
  • Richard Finney
    Senior Member
    • Feb 2009
    • 701

    #2
    Instead of
    chmod +x /home/cmccabe/Desktop/NGS/bedops-2.14.4/bin*

    try
    chmod +x /home/cmccabe/Desktop/NGS/bedops-2.14.4/bin/*

    note added slash at end of of "bin"

    Comment

    • ECO
      --Site Admin--
      • Oct 2007
      • 1360

      #3
      I'd double check the permissions. Your chmod would've missed the files you're interested in. Try this:

      chmod -R 755 /home/cmccabe/Desktop/NGS/bedops-2.14.4/bin/

      Comment

      • cmccabe
        Senior Member
        • Jul 2012
        • 355

        #4
        Thank you that worked .

        Comment

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