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 <bhaas@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
>

> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/