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Hi all,

Andreas Tille wrote:
More to the point, I have created a set of diffs against the 3.7 codebase, which when applied will merge in all of my changes to the 3.7 code:

Just downloaded and I will see how we might be able to base a Debian
package on it.
I made some further changes yesterday to move libmuscle into a c++ namespace in order to avoid global namespace pollution. A new diff is here:
The diff does not include source for files I added, such as the thread storage class and the anchored profile-profile alignment function.

Robert, I would be delighted if you would consider basing future muscle releases around the library refactorization. Please let me know what else I can do to facilitate it.

I would totally support this.

BTW, Aaron, libGenome is now an official Debian package as you can see at

that's good news, it seems we are progressing :)

Moreover I noticed that we might get some name space polution with Mauve:
Please have a look at


I do not know this other mauve project but wt least we might possibly
have to change the package name of your Mauve in Debian in case we
can not convince the other maintainer to change the name.  Could you
perhaps suggest a useful name for the Debian package?  I'd consider
something like wisc-mauve or something like this reasonable, but perhaps
you have a better suggestion.  Once we are at it: Do you have any
hint for my problem with a missing jar file when trying to build Mauve?
Hmmm, that's unfortunate. Yes, I had come across their project before but never really considered that it might cause naming conflicts. Perhaps they would want to rename to something like mauve-test? Or maybe the aligner could be renamed mauve-aligner? I'd prefer to avoid wisc-mauve since I'm now at the University of Queensland and Mauve may move at some point.

As for the mauve build error, some further investigation suggests that the PropertyFile task lives inside ant-nodeps.jar, which should be included in the ant-optional debian package. Perhaps ant can't find /usr/share/ant/lib/ant-nodeps.jar ? If that file exists you might try running:
ant -lib /usr/share/ant/lib/ant-nodeps.jar
and if that works, then ant may not know where $ANT_HOME is, or $ANT_HOME may not be set to /usr/share/ant.


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