THANK YOU!!! :)

The fundamental piece that I was missing at:
https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes

was the

<command>someTool.sh $input1 ${os.path.join( input1.extra_files_path,
'results.txt' )} ${os.path.join( input1.extra_files_path,
'results.dat' )} $output1</command>


It would be great if the documentation could be updated a bit for clarity
on the importance of the '.extra_files_path', such as 'important: your tool
needs to create this directory and store the additional files that you want
there'.

This is a big leap forward for me. I'll now get on to testing the other
aspects of it. (still climbing the galaxy learning curve).

thanks again!

~brian




On Mon, May 18, 2015 at 2:39 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:

> 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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>


-- 
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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