[Debian-med-packaging] Bug#476626: clustalw: -outfile option does not work

[Charles Plessy]

reassign 476626 emboss
retitle 476626 emboss: emma does not work with clustalw > 2.0
thanks

Le Fri, Apr 18, 2008 at 10:48:04AM +0900, Charles Plessy a écrit :
> Severity: important
> 
> User report on EMBOSS mailing list (
> http://lists.open-bio.org/pipermail/emboss/2008-April/003253.html )
> prompted me to check the situation of our packaged version of clustalw.
> 
> Indeed the 'emma' wrapper does not work with clustalw 2.04 or 2.05. I
> quickly found out that the -outfile option of clustalw is broken. I
> think that this causes the problem and will report the bug in upstream's
> bugzilla.

After checking clustalw 1.83, there is no obvious regression: -outfile
works, but only for the alignment file, and I was fooled by the fact
that in the absence of the -newtree option, clustalw was trying to write
the .dnd file in the read-only directory from which I read the sequences
to align.

The problem is more probably with emma, the EMBOSS wrapper for clustalw.

-- 
Charles Plessy
http://charles.plessy.org
Wakō, Saitama, Japan