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How to apply maven build system (Was: How to use Debian packaged freehep instead of upstream provided freehep.jar)


inspired by some hints about Java packaging I tried another package.  It
is called patristic[1] (just another biological phylogeny software).  It
comes just with a directory full of *.java files and the binary download
just tells in what directory layout the classes should end up.  Chances
to contact upstream seem low (Homepage mentioned on the scientific
publication page[2] is not available any more).  So I decided to start
some maven training and did

  mvn archetype:generate -DgroupId=Patristic -DartifactId=patristic -DarchetypeArtifactId=maven-archetype-quickstart -DinteractiveMode=false

as it is suggested here[3]
> Anyway, unfortunately, you still have to put hands on upstream's code,
> because maven requires the projects it's working on to have a specific
> directory structure.

That's fine in the case of patristic - I'd need to repack the code in
any case - so why not applying the maven directory layout?
I'm actually not very keen on really using maven as long as I can
get the package working at all - but I actually have no real clue
what command line would trigger the build process (and upstream)
seems to be dead.  So in principle the most simple help would be
a command line which builds the JAR.

Kind regards and thanks for your patient help


[1] ftp://ftp.bioinformatics.org/pub/patristic/Patristic-src.tar.gz
[2] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1352388/
[3] http://maven.apache.org/guides/getting-started/maven-in-five-minutes.html


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