Re: Packaging Mauve and libClustalW
On Fri, 14 Mar 2008, Aaron Darling wrote:
Yes, libMUSCLE and libClustalW provide redundant functionality from Mauve's
point of view. The libMems codebase had been relying on clustalw for a few
functions, and as of today I have removed those dependencies and updated
libMems and mauveAligner accordingly. It should now be possible to build
everything without libClustalW.
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?
2. libClustalW: For those who want to test there are unofficial
packages available at
http://people.debian.org/~tille/packages/libclustalw/
--> Note: These packages will not become official because
of the licensing issues.
3. libMems: Based on the archive downloadable at
http://gel.ahabs.wisc.edu/mauve/source/mauve_2.1.1/
which depends from libClustalW you can test my
unofficial packages from
http://people.debian.org/~tille/packages/libmems/
--> Note: libMems packages will be uploaded to Debian
once the dependencies (either libCLustalW or libMuscle)
are solved.
4. mauveAligner: Unofficial packages at
http://people.debian.org/~tille/packages/mauvealigner/
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?
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.
When you talk about libMUSCLE as replacement for libCLustalW you are
probably refering to the files in the snapshot directory
http://gel.ahabs.wisc.edu/mauve/source/snapshots/
right? 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)?
If it would be helpful I would volunteer to add the Makefile.am stuff
that is needed to build the muscle binary.
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
-/usr/share/ant/lib
-/home/tillea/.ant/lib
-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.
Kind regards
Andreas.
--
http://fam-tille.de
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