Re: Packaging Mauve and libClustalW (sorry for posting twice)

[Andreas Tille <tillea@rki.de>]

Hi,

thanks to my stupidity I had debian-devel list in my first mail
which is _wrong_.  Please respond to debian-med@lists.debian.org.

For other reader of the list here comes the content ...


[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
      http://people.debian.org/~tille/packages/libclustalw/
     and
      http://people.debian.org/~tille/packages/libmeme/
     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
      http://gel.ahabs.wisc.edu/mauve/source/mauve_2.1.1/

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 AUTHORS:
    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 ;-))

          Andreas.

--
http://fam-tille.de


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