mafft on remote cluster

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seeholz...@gmail.com

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Apr 30, 2015, 7:05:53 PM4/30/15

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Hi all,

I'm trying to get AftrRAD running on a remote cluster for which I do not have root privileges to install mafft. I've installed mafft in my home directory instead. Do I have to specify a path to mafft when running AftrRAD or do I just move the executable to the working directory?

Thanks!

Glenn

Mike Sovic

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Apr 30, 2015, 10:04:02 PM4/30/15

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Hi Glenn,

I'm not really sure about this. I see some instructions for installation without root privileges here...

http://mafft.cbrc.jp/alignment/software/installation_without_root.html

Is this what you've already done?

If so, you might be right that you need to specify a path to the executable in the AftrRAD script. If you're using the standard version (v4.1), you can specify this at line 2337 - just replace 'mafft' with the path to the executable. If you're using the paralleled version, it's at line 3543.

I'd probably test it out on the example dataset (which is small and will run quickly) both ways - first try it as it is, and if you get an error, try editing the script by adding the path to the executable. Let us know what happens, and if anyone else has thoughts on this, please do let us know.