[EMBOSS] Standalone Jemboss: where does output go?

[humberto at hpcf.upr.edu]

I'm one of the co-developers of bioknoppix. We've set up a standalone Jemboss 
on the CD, and one of our users sent us a note that Jemboss ran and didn't 
produce output.

The Jemboss makefile contains the follwing fragment:

echo "(cd $(prefix)/share/$(PACKAGE)/jemboss; java org/emboss/jemboss/Jemboss 
&)" >> $(bindir)/runJemboss.csh;

but mere mortals don't have write access to $(prefix)/share/$(PACKAGE)/jemboss 
(actually, on our CD, neither does ROOT).

Removing the cd command allows text output to work.

Graphical programs just dump a bunch of png files into the current directory. 
Is this expected behavior or did we break something?

-- 
Humberto Ortiz Zuazaga
Programmer-Archaeologist
High Performance Computing facility
University of Puerto Rico
http://www.hpcf.upr.edu/~humberto/


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