Question: Installing new MAFFT version
gravatar for Ghoti
3.0 years ago by
Ghoti70 wrote:

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:

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).

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.

mafft • 2.4k views
ADD COMMENTlink modified 2.8 years ago by Biostar ♦♦ 20 • written 3.0 years ago by Ghoti70

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.

ADD REPLYlink written 3.0 years ago by Joe18k

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.

ADD REPLYlink written 3.0 years ago by Ghoti70

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

ADD REPLYlink written 3.0 years ago by _r_am32k

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

ADD REPLYlink written 3.0 years ago by Ghoti70
gravatar for Ghoti
2.9 years ago by
Ghoti70 wrote:

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

ADD COMMENTlink written 2.9 years ago by Ghoti70
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