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RE: Packaging Mauve and libClustalW

Was this intended for me? If so, I'm not clear why...

-----Original Message-----
From: Andreas Tille [mailto:tillea@rki.de] 
Sent: Wednesday, March 12, 2008 3:16 PM
To: Debian Developers
Cc: Aaron Darling; Robert C. Edgar Bob; Todd J Treangen
Subject: Re: Packaging Mauve and libClustalW

[Robert and Todd please read below about some issues about muscle]
Everybody: PLease keep the debian-med mailing list in CC.  We would like to
build reasonable Debian packages out of a uniform source that contains all
features that are needed and as less bugs as possible.  The Debian-Med
mailing list might serve as a common discussion forum to avoid a fork.

On Thu, 14 Feb 2008, Charles Plessy wrote:

> I had a very quick look to the sources, and I am wondering if mauve 
> can work with muscle instead of clustalw. This would solve the licence 
> problem. However, it needs a specific patch on Muscle. I can try to 
> submit it to Muscle's upstream if necessary. Otherwise, it may be 
> possible to build two different binary packages from the same source 
> pacakge (like vim or centericq).

I would like to have a quick update onto Mauve issues:

   1. Packages for libGenome are just uploaded the day before yesterday.
      I expect it to be available at the Debian Mirror soon.
   2. To prepare at least local Mauve packages I continued to package
      libClustalW and libMeme (which depends from both) and putted my
      efforts to
      Where the later one is also in our SVN because it can be distributed
      easily once the preoconditions (either a clean libClustalW or
      the libMuscle replacement mentioned above are available.
   3. My next step should be

Aaron, a new library tarball libMUSCLE-1.0.0.tar.gz occured at this location
for version 2.1.1 and while you used version 1.0.0 you mention in the file
     It contains bugfixes and new features to the original 3.6 code. But
upstream now has version 3.7.  So I _really_ like your atempt to build a
library and I would love to convince the muscle authors to build their
binary linked against this library, but I'm afraid by the current approach
we might end up with a fork. :-(

Could you please clarify things.  My prefered way to go would be:

   1. Take the latest Muscle upstream source (including patches for
      gcc 4.3)
   2. Choose a new version number.
   3. Change the build process using automake / libtools to build
      a dynamic and static library from muscle code and link the
      executable against this library.
   4. Link Mauve binary against this library.

I'd volunteer to provide any help that might be needed but please try to
avoid confusing your users by using different versions that have good
chances to drift away from each other.

Aaron, just for the sake of my private packaging: Do I understand things
right that your libMUSCLE is a replacement for libClustalW and I might be
able to drop libClustalW in favour of libMUSCLE? My plan is to work on Mauve
Debian packages in my private repository until the issues above will be
solved nicely.

Kind regards and please remember to keep the Debian-Med list in CC to have a
record for all other potential packagers in our crew.  (I'm happily not
alone ;-))



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