[EMBOSS] Jemboss and emma

[Brett Kaufman]

I have been trying to get Jemboss to run emma.  I find a number of 
issues that I haven't tracked down:
1) cannot open sequence files (.fasta).  these same files can be read 
and emma executed via terminal.
2) can read pasted .fasta sequence, and the output of emma viewed in 
results, but no file can be saved.
3) as no file is "opened" by Jemboss, I cannot employ prettyplot to 
shade the alignment

Other issues:
1) prettyplot cannot open a .msf file.  Any .msf, even those generated 
by emma.

I know that the input files are valid because they can be used in 
terminal, or embossRUNNER.  I expect there to be a problem with my 
settings or Jemboss combile.

I am including my jemboss.properties and runJemboss.csh files.  Any 
insight would be greatly appreciated!
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Thanks in advance,
-Brett