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
snapshot.
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.
Right.
there are three main programs: mauveAligner, progressiveMauve, and
procrastAligner
OK.
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
myself.
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.
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
Andreas.
--
http://fam-tille.de
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