Question: Symbolic Link To Bowtie
0
gravatar for Luciano Cosme
7.2 years ago by
Luciano Cosme220
Luciano Cosme220 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
alignment bowtie • 1.3k views
ADD COMMENTlink modified 7.2 years ago by Jennifer Hillman Jackson25k • written 7.2 years ago by Luciano Cosme220
0
gravatar for Jennifer Hillman Jackson
7.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
ADD COMMENTlink written 7.2 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 94 users visited in the last hour