[EMBOSS] Antwort: Re: EMBOSS Digest, Vol 13, Issue 4

ajb at ebi.ac.uk ajb at ebi.ac.uk
Tue Aug 8 10:00:59 UTC 2006

Hello David,

> 2)
> Unfortunately this won't help much, because there seems to be a problem
> with emma also in the new windows version.

I can't reproduce the problem.

> emma is not a full application, but only an interface to the multiple
> alignment program clustalW.
> The current windows version of EMBOSS contains an clustalw executable, but
> this doesn't work. (Error message I get: "The system cannot execute the
> specified program").

Well that's definitely a Microsoft error message rather than an EMBOSS
one.  I have tried the clustalw.exe supplied with EMBOSS-MS on a few
Windows setups on a range of machines just now. None showed that
error.  Admittedly some of the machines required the vcredist_x86.exe
Visual C/C++ 2005 runtime libraries added but that was mentioned in
the announcement (and I've just put a README.win on the ftp server
saying the same). Besides, that would usually give a "Missing DLL"
error, not the "Cannot Execute" one. I do find it odd that
clustalw.exe gives that error but the emboss applications do not: they
were all built using the same compiler on the same machine.

DependencyWalker (http://www.dependencywalker.com) shows that the
required modules on XP for clustalw are kernel32.dll, msvcr80.dll,
msvcrt.dll and ntdll.dll. You could try installing Dependencywalker
and seeing whether it detects any missing modules for clustalw on
your system.

Does the problem occur on your home XP installations, your Schering
installation or both?

> I replaced it with the XP executable from
> ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/ but now I'm getting a
> different problem.
> The clustalw used directly runs without problem. But if called from emma
> it complains:
> CLUSTAL W (1.83) Multiple Sequence Alignments
> Error: unknown option /-infile=00002432A
> Error: Failed to open filename '00002432B'
> Problem writing out EMBOSS alignment file
> clustalw needs just /infile= and not /-infile=

Yes, it would do that :-) Versions of clustalw for Windows found on the
network usually do not have the UNIX-style command line. You must use the
clustalw.exe supplied with EMBOSS-MS which does have the UNIX
command line.

> Btw. I could not reproduce the Path overwriting on any generic XP (Pro or
> Home) so it has something to do with our local XP installtion but I could
> not find the reason so far.

I'm still intrigued by that one. I expect that you've checked that
there isn't another program called setenv.exe on the system?



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