Hi Brian,

In your example tool, you need to pass “${ test_cdt.files_path }" to your perl 
script, which is a not-yet-existing directory for the files you want to be part 
of the dataset’s extra files path. 
Then you create that directory and place the files you want within that 
directory.



Thanks for using Galaxy,

Dan


On May 18, 2015, at 2:02 PM, Brian Haas <bh...@broadinstitute.org> wrote:

> 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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