Re: [RFS] clustalw

[Aaron Darling <darling@cs.wisc.edu>]

Charles Plessy wrote:
> Le Thu, Mar 06, 2008 at 07:26:53AM +0100, Andreas Tille a écrit :
>   
> > On Thu, 6 Mar 2008, Charles Plessy wrote:
> >
> >     
> > > The package for Clustal W 2.0.3 is ready.
> > >       
> > Thanks.
> > Without having had a look into the packaging: Is there any chance to
> > build a separate libclustalw from this source that would also work
> > together with Mauve?
> >     
>
> Well, it is a few releases ahead. I suggest Aaron to contact upstream,
> especially that libclustalw is infringing the license of Clustal W. We
> can not distribute it unless an agreement is found. This would also be
> an opportunity to reduce the diff between the two branches as much as
> possible.
>   
Hello all,

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:
******************************************************************************

                 POLICY ON COMMERCIAL DISTRIBUTION OF CLUSTAL W

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.

******************************************************************************

Since I do not distribute libClustalW or Mauve commercially, I believe I 
am within the scope and spirit of the license.  If the original clustalw 
authors feel otherwise, however, they are welcome to contact me.  I 
probably did misstep by not including the license in a file when I 
refactored it into a library.  I've now committed the license to the 
source code repository.


Sorry, haven't had time to make an official libGenome release yet.  I 
will do it in conjunction with the next official Mauve release.  This 
could take some time (weeks?)

-Aaron