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Re: [RFS] clustalw

Le Thu, Mar 06, 2008 at 09:00:49PM +1000, Aaron Darling a écrit :
> The mauveAligner codebase depends on the library refactorization of 
> clustalw 1.83.  I believe the new 2.x series of clustal releases was 
> rewritten from scratch.  Although I have not checked, I would assume 
> that the internal structure would be quite different to 1.83 and that it 
> would be much more work to refactor 2.x into a library than it would be 
> for me to remove the current dependency on clustalw altogether.
> That said, I investigated the licensing of the clustalw 1.83 codebase 
> from which libClustalW derives.  I found this statement at the top of 
> the readme:
> ******************************************************************************
> Clustal W is freely available to the user community. However, Clustal W is
> increasingly being distributed as part of commercial sequence analysis
> packages. To help us safeguard future maintenance and development, 
> commercial
> distributors of Clustal W must take out a NON-EXCLUSIVE LICENCE. Anyone
> wishing to commercially distribute version 1.81 of Clustal W should 
> contact the
> authors unless they have previously taken out a licence.
> ******************************************************************************

Hello again,

I looked at Clustal W 2.0.3, and indeed it seems that it was rewritten
from scratch in C++. So from the point of view of code duplication,
libClustalW would be perfectly acceptable in Debian.

However, for the license, I still have doubts. Some versions earlier and
later than 1.83 explicitely forbid modification. Also, by default
copyrighted work is "all rights reserved", so if the right of modifying
the work is not given, it is safer to assume that modification is not
allowed. Our archive maintainers are more ferocious than most academic
reviewers, and I am affraid that a libclustalw package would be rejected
by them if we have no clarification. For this reason, I have asked the
question to the Clustal W authors (actually earlier in February, and I
am waiting for their answer).

>From the point of view of the prospective Debian package for Mauve, it
would be beneficial to make the dependancy on libClustalW optional: this
would allow us to distribute it in the "main" section of Debian, instead
of the "contrib" section (provided that Mauve would not depend on other
works that do not comply with the Debian Free Software Guidelines), wich
is not stricto sensu part of the Debian operating system (for instance
it is not on the CDs/DVDs). This is also something to take into account.

Have a nice day,

Charles Plessy,
Debian-Med packaging team
Wakō, Saitama, Japan

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