Installing new MAFFT version

Question

[Ghoti]

I'm trying to update my MAFFT version without overwriting the existing version (it's difficult for me to get root access). I've created a pseudo bin folder to contain the new MAFFT files, but I seem to be unable to specify priority of the new MAFFT location (defaults to /user/local/bin). When I do call the new MAFFT version (even when renamed), I receive the following error:

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v7.310 != v7.385 (2018/Feb/3)

There is a problem in the configuration of your shell. Check the MAFFT_BINARIES environmental variable by $ echo $MAFFT_BINARIES

This variable must be *unset*, unless you have installed MAFFT with a special configuration.  To unset this variable, type $ unset MAFFT_BINARIES or % unsetenv MAFFT_BINARIES Then retry $ mafft input > output

To keep this change permanently, edit setting files (.bash_profile, .profile, .cshrc, etc) in your home directory to delete the MAFFT_BINARIES line. On MacOSX, also edit or remove the .MacOSX/environment.plist file and then re-login (MacOSX 10.6) or reboot (MacOSX 10.7).

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Should I change my environment path to include my pseudo bin desktop folder? Won't that still leave a conflict between the original local bin? I'm relatively new to bash and unfamiliar with this sort of problem.

[Joe]

Ordinarily it would be enough to prepend the 'personal' directory for mafft to your $PATH. e.g. export PATH=/home/ghoti/bin:$PATH (or whatever).

It looks like Mafft is a bit more thorough in its binary locating though, rather than just relying on order of precedence in the PATH, it actually wants an environment variable to point at it. In which case, I suspect you'll have to follow their instructions and edit these accordingly, but you could try just setting your PATH up first.

[Ghoti]

Thanks for the suggestion. I'll try to prepend the directory to $PATH and hope it prioritizes based on order while also changing the mafft file name slightly to better distinguish the two versions. I've been navigating to the appropriate directory and issuing an authoritative command (./mafft), which produced the error code above, suggesting the environmental variable is an issue. Will look for specific documentation.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

[Ghoti]

Wasn't sure if code formatting was appropriate for an error report. Thanks for correcting.

Answer 1

[Ghoti]

A simple change to the Makefile fixed the problem, documented here.