It is a wiki, if you miss something - please add it.

Thanks

Martin

On Mon, May 18, 2015 at 3:08 PM Brian Haas <bhaas@broadinstitute.org> wrote:

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 <dan@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 <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
>

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--

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

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