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" <[EMAIL PROTECTED]> 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 > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
