[EMBOSS] jemboss standalone installation problems on MacBook/Intel

[Tim Carver]

Hi Robert

Jemboss has not been set up to work with fink. You do need to use the EMBOSS
download (including any patches) and install using the script as described
at:

http://emboss.sourceforge.net/Jemboss/install/standalone.html

Also make sure you have the latest java from:

http://www.apple.com/downloads/macosx/apple/j2se50release4intel.html

Regards
Tim Carver


On 12/12/06 22:32, "Robert Wohlhueter" <bobwohlhueter at earthlink.net> wrote:

> 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
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss