Re: Packaging Mauve and libClustalW
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:
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)
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
there are three main programs: mauveAligner, progressiveMauve, and
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
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.
I think you need to install the ant-contrib jars, which might already be
packaged for debian?
Finally I tried to build Mauve but failed:
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
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.
hope that helps,