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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