Hello Luciano,

You probably need to be root to write to /bin (often done by leading the command string with a "sudo"). It depends on how your system is set up. But you don't need to put bowtie at the top level /bin, it doesn't really belong there as a higher global function. It can go in a lower level bin, often organized such as:


/<some_path_from_root>/<optional>x86_64/bin/bowtie

This kind of location is likely already in your $PATH. May still require sudo permissions, a check-in with your sys admin is advised.

Wiki help for installing 3rd party & NGS tools/data to be used by Galaxy:
http://wiki.g2.bx.psu.edu/Admin
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

Best wishes,

Jen
Galaxy team

On 7/27/11 4:38 PM, Luciano Cosme wrote:
Hi,
    I am running Galaxy locally (Ubuntu 11.04) and I am getting this
error message when I try to use mapping with bowtie:

Error indexing reference sequence
/bin/sh: bowtie-build: not found

    Then I downloaded bowtie and tried to create a symbolic link using
at /bin:
ln -s /home/koala2/bowtie bowtie

    Then I get this error message:
ln: creating symbolic link `bowtie': Permission denied

    I know that is more a linux issue than Galaxy, but does anyone have
any suggestion? I changed the permission of bowtie folder and file but
keep getting same error. I am logged as administrator too.

Thank you.

Luciano




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