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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
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use the Galaxy Development list:
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