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Question: Symbolic Link To Bowtie
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gravatar for Luciano Cosme
7.3 years ago by
Luciano Cosme • 220
Luciano Cosme • 220 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
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modified 7.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.3 years ago by Luciano Cosme • 220
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gravatar for Jennifer Hillman Jackson
7.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 7.3 years ago by Jennifer Hillman Jackson ♦ 25k
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