[Biopython-dev] [Bug 2815] Bio.Application command line interfaces

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sat May 9 16:40:27 UTC 2009


------- Comment #31 from cymon.cox at gmail.com  2009-05-09 12:40 EST -------
(In reply to comment #30)
> I've got test_Mafft_tool.py working on one Linux machine using MAFFT v6.626b
> (2009/03/16) installed from source.

That was my reference installation when writing the command line tool (on
Jaunty/RHE 5.3).

> However, test_Mafft_tool.py fails on another Linux machine using MAFFT v6.240
> (2007/04/04) installed using the distribution's package, in this case Ubuntu
> Jaunty:
> http://packages.ubuntu.com/jaunty/mafft
> Note that the next version of Ubuntu currently also uses the same old package:
> http://packages.ubuntu.com/karmic/mafft
> As does Debian unstable:
> http://packages.debian.org/unstable/science/mafft
> From trying mafft v6.240 by hand at the command line, it never seems to
> actually print anything to the console.  Either the MAFFT API changed (which
> doesn't seem to be the case), or the version Ubuntu installed on this machine
> is broken.  This could be due to something else like the version of awk or gcc
> (guesses based on the MAFFT change log):
> http://align.bmr.kyushu-u.ac.jp/mafft/software/

Hadn't tried the Ubuntu package...

On the upside, the Muscle3.7 package installed from Ubuntu passes our tests,
whereas the source compiles but core-dumps. Similarly, ProbCons1.2 won't
compile but the Ubuntu package looks good (havent written the tests yet).

> Note that the latest version is now MAFFT 6.704, so we should try that too. If
> I am right about the current Ubuntu/Debian package being broken, we should get
> in touch with them about updating it... otherwise we can look forward to bug
> reports about our wrapper and/or test_Mafft_tool.py failing.

Built from source on Jaunty; it passes our tests.

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