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Re: Packaging Mauve and libClustalW

On Fri, 21 Mar 2008, Aaron Darling wrote:

I have added a doxygen target to libGenome and the rest of the libraries. I used the doxygen m4 and automake macros that are floating around online which seemed far more sensible than cobbling together my own solution. To build the docs, simply run:
make doxygen-doc
and docs will appear in the doc/ directory

Great.  I think I'll probably base a new package of libGenome onto this

I was contacted by Des Higgins and we straightened out the licensing issues. It sounds like they are probably fine with having clustal packaged as a library, but I have removed the dependency on libClustalW anyways so the point is moot.


there are three main programs: mauveAligner, progressiveMauve, and procrastAligner


That sounds reasonable. I took a brief look to see whether doxygen could be abused to make man pages for programs instead of just source code but didn't immediately see how it could be done.

Well, I think writing three man pages when explicite command line help is
given is not so much effort.  I think I could do the writing from time to
time when the packages of the libraries are building.  I'll provide you
with this in the beginning of April I think.

As mentioned in a previous message, I just finished this task.

Yeah. Great job!

Your help would be welcome. I have included a target to build the binary as part of the library's Makefile.am, but I seem not to have gotten it right because automake doesn't figure out the dependencies until the second time I run make.

I'll try to check this.  I had done this in the past and remember that there
was some magic but I know that there are some people hanging around on
Debian lists who have good experience if I can not sole the magical problems

Finally I tried to build Mauve but failed:

/usr/lib/jvm/java-6-sun/bin/java -classpath /usr/share/ant/lib/ant.jar:/usr/share/
Buildfile: build.xml

BUILD FAILED /home/tillea/debian-maintain/todo/mauve/mauve/mauve-2.1.1/build.xml:47: Problem: failed to Cause: the class org.apache.tools.ant.taskdefs.optional.PropertyFile was not found. This looks like one of Ant's optional components. Action: Check that the appropriate optional JAR exists in
        -a directory added on the command line with the -lib argument

Do not panic, this is a common problem. The commonest cause is a missing JAR.

This is not a bug; it is a configuration problem

Any hint which particular JAR file would help here?  I'm completely
unexperienced with Java.
I think you need to install the ant-contrib jars, which might already be packaged for debian?

I think it is called ant-optional and I have installed it but I can
try my luck once more.  Perhaps you could foreward me the command line
you are using and a build log by private mail?

Kind regards and many thanks for your cooperation



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