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

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2815





------- Comment #30 from biopython-bugzilla at maubp.freeserve.co.uk  2009-05-09 07:59 EST -------
I've got test_Mafft_tool.py working on one Linux machine using MAFFT v6.626b
(2009/03/16) installed from source.

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/

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.


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