Hi Peter,

I'm actually more confused now that I was when I started...  I was able to
get your code working, focusing on the 'makeblastdb' with a nucleotide
fasta file.  I figured that experimenting with this example would lead to
some key insights, particularly by dropping certain files that are stored
as extra-files area.   I copied everything over as a new tool, made it a
new data type, and trimmed the blast.py code down to the bare essentials
for testing just the nucleotide makeblastdb functionality. However,
commenting out 'self.add_composite_file()' for various files had no effect
- the files were still being stored.   I then make 'composite_type = None'
and it still stored the files to my dismay.

Since I couldn't get my copy to work as I had expected, I went back over to
your 'blast.py' and just commented out the
''self.add_composite_file()' lines and set 'composite_type = None' .... and
no effect.

Of course, I restarted galaxy after each modification, and could verify
that it was reading the new files and had byte-compiled the py mods.

I'm clearly not grasping something fundamental here.  I can't get my code
to bundle files, and I can't get your code to *not* bundle files. ;)

Any ideas on where to go to troubleshoot this further?

many thanks,

~brian
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