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 usingat /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 haveany 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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