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Re: Packaging Mauve and libClustalW

Hello Andreas,

Andreas Tille wrote:

Ahh, thanks for the update.  This is good news.  For the record:

  1. libGenome: Is ready packaged and uploaded to incoming.  I expect
                it to be available from Debian mirror in the beginning
                of next week.
                I tried to find out how to generate doxygen docs but
                failed. Would you mind adding a make target to create
                the doc or at least tell me what magicall command has
                to be issued to create the docs?

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

  2. libClustalW: For those who want to test there are unofficial
                packages available at
           -->  Note: These packages will not become official because
                of the licensing issues.

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.

  3. libMems:   Based on the archive downloadable at
                which depends from libClustalW you can test my
                unofficial packages from
           -->  Note: libMems packages will be uploaded to Debian
                once the dependencies (either libCLustalW or libMuscle)
                are solved.
  4. mauveAligner: Unofficial packages at
                needs libraries 1. - 3. installed and will be uploaded
                once the dependencies are available.
           -->  Note: Man pages have to be written.  Uhmm, there are
                a lot of tools inside that often just issue a short
                Usage notice.  Are all these tools intended to be
                run from the command line or are there only the two main
commands progressiveMauve and mauveAligner as user interface?

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

                In this case I would like to "hide" all the binaries
                in /usr/lib/mauveAligner and use wrappers that will
                set the PATH to this dir.  This would reduce the amount
                of man pages to write reduce to two (for which the
                docs are more verbose and the command line help is
                really existent.

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.

When you talk about libMUSCLE as replacement for libCLustalW you are
probably refering to the files in the snapshot directory




I would like to wait a bit until I have some chance to estimate
how much time it will consume to find a clean solution for libMuscle
with upstream.  While the solution with libMuscle is clean regarding the
licensing I would love to see the project growing reasonable with a
joined libMuscle development team which probably would have a good side
effect.  Would you regard it possible without large effort to merge
your changes with the latest MUSCLE release (0.37, perhaps SVN)?

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

If it would be helpful I would volunteer to add the Makefile.am stuff
that is needed to build the muscle binary.

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.

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?

hope that helps,

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