[EMBOSS] jemboss standalone installation problems on MacBook/Intel

[Robert Wohlhueter]

Trying to run emboss/jemboss as a standalone on MacBookPro/intel under
OS 10.4.  Downloaded and installed from fink.sourceforge.net (in fink's
preferred /sw/share/EMBOSS tree).  [In trying to circumvent the proglems
described below, I also built, in the /usr/local tree, from source code
at emboss.sourceforge.net, an entirely separate installation.  I get
exactly the same set of errors with that installation.]

Facts as best I comprehend them:
1) the envvars, including CLASSPATH, JEMBOSS_HOME, EMBSS_INSTALL, etc.,
are set as specified in $EMBOSS_INSTALL/jemboss/runJemboss.sh, and seem
correct to me.  jars, *.class, *.java, and the several executables that
comprise the emboss suite of applications, as near as I can tell are all
present.

2) java runtime is that bundled by Apple with OS 10.4, namely
   {summer:~}66 bobw$ java -version
   java version "1.5.0_06"
   Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_06-112)
   Java HotSpot(TM) Client VM (build 1.5.0_06-64, mixed mode, sharing)

3) As suggested in Emboss Administrator's Guide, testing the
installation with
   $ wossname -auto
works as expected, listing countless applications in various categories.

4) When I try to run `java $JEMBOSS_HOME/org/emboss/jemboss/Jemboss local &`
   {summer:~}68 bobw$ jemboss
   [1] 736
   {summer:~}69 bobw$ Exception in thread "main"
java.lang.NoClassDefFoundError:
       /sw/share/EMBOSS/jemboss/org/emboss/jemboss/Jemboss
I'll worry about this later.

5) The nub of the problem is when I run `java org.emboss.jemboss.Jemboss
local &` from JEMBOSS_HOME, I get the following messages:

{summer:/sw/share/EMBOSS/jemboss}60 bobw$ Exception in thread "Thread-2"
java.lang.NullPointerException
       at
org.emboss.jemboss.gui.BuildProgramMenu$1.construct(BuildProgramMenu.java:278)
       at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127)
       at java.lang.Thread.run(Thread.java:613)

I'm not a java programmer, but when I look at source code in
BuildProgramMenu.java, it looks like the error arises in a routine which
is trying to construct a "dataFile" file specification from data in a
object called "mysettings".  I don't see how/where "mysettings" is
defined, but I'm suspicious that it is intended to read data from my
local settings (envvars, emboss.defaults ??), is not able to, and thus
passes null information to the new datafile specification.

Can anybody elucidate the source of data in "mysettings" and give me a
hint what I need to do to supply it?

Thanks for any and all pointers,

Bob Wohlhueter