18 May
2015
18 May
'15
2:09 p.m.
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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>> >
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>>
>>
>
>
> --
> --
> Brian J. Haas
> The Broad Institute
> http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
>
>
> ___________________________________________________________
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>
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