>From some more testing it appears that the generate_primary_file() is
called when a user manually uploads a composite data type (cdt), but it's
not called when the cdt is generated as a product of a run. That's fine.
I can work around that.
I am curious about how cdts are uploaded manually, tho
I've updated my code, which now generates the .extra_files directory:
https://github.com/brianjohnhaas/galaxy_composite_datatype_test
I'm now trying to get the
composite_type = 'auto_primary_file*' *to work, but all I'm getting is an
empty file. My module code simply includes:
class Composite
Ah! will do. :)
On Mon, May 18, 2015 at 3:09 PM, Martin Čech wrote:
> It is a wiki, if you miss something - please add it.
>
> Thanks
>
> Martin
>
>
> On Mon, May 18, 2015 at 3:08 PM Brian Haas
> wrote:
>
>> THANK YOU!!! :)
>>
>> The fundamental piece that I was missing at:
>> https://wiki.gal
It is a wiki, if you miss something - please add it.
Thanks
Martin
On Mon, May 18, 2015 at 3:08 PM Brian Haas wrote:
> THANK YOU!!! :)
>
> The fundamental piece that I was missing at:
> https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes
>
> was the
>
> someTool.sh $input1 ${o
THANK YOU!!! :)
The fundamental piece that I was missing at:
https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes
was the
someTool.sh $input1 ${os.path.join( input1.extra_files_path,
'results.txt' )} ${os.path.join( input1.extra_files_path,
'results.dat' )} $output1
It would be
Hi Brian,
In your example tool, you need to pass “${ 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.
Than
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 s
I've uploaded my simple example here:
https://github.com/brianjohnhaas/galaxy_composite_datatype_test
I can't seem to get it to bundle the output files no matter what I've
tried. Help is much appreciated. :)
best,
~brian
___
Please keep a
Fantastic!
I've actually made a few changes. I'm putting my latest code up on github
now and will share it in just a moment. It'll be much easier this way -
as you suggested.
best,
~brian
On Mon, May 18, 2015 at 9:58 AM, Peter Cock
wrote:
> Hi Brian,
>
> Your original email with attachme
Hi Brian,
Your original email with attachments has made it to the list now,
http://dev.list.galaxyproject.org/difficulty-creating-composite-data-type-tp4667193.html
Title: "difficulty creating composite data type"
Peter
On Mon, May 18, 2015 at 2:25 PM, Brian Haas wrote:
> In the next couple of
In the next couple of hours, if I'm not able to resolve this, I'll post my
ultra-simple example on github and I'll be grateful for others to take a
look.
cheers,
~brian
On Mon, May 18, 2015 at 9:23 AM, Peter Cock
wrote:
> On Mon, May 18, 2015 at 1:55 PM, Brian Haas
> wrote:
> > Thanks, Peter!
On Mon, May 18, 2015 at 1:55 PM, Brian Haas wrote:
> Thanks, Peter! I've verified that I can get your code to work - bundling
> the composite files. I'll keep plugging away at my little example and see
> if I can figure out what's going awry.
>
> more later. Thx again!
Good luck - compound da
Thanks, Peter! I've verified that I can get your code to work - bundling
the composite files. I'll keep plugging away at my little example and see
if I can figure out what's going awry.
more later. Thx again!
~brian
___
Please keep all r
On Sun, May 17, 2015 at 5:44 PM, Brian Haas wrote:
> Greetings.
>
> Does anyone per chance have a simple working example of using composite data
> types? I've gotten as far as I can with the galaxy documentation, and I
> can't seem to get the additional files bundled into an extra files
> direct
Greetings.
Does anyone per chance have a simple working example of using composite
data types? I've gotten as far as I can with the galaxy documentation,
and I can't seem to get the additional files bundled into an extra files
directory.
(note, I have my example submitted w/ files attached, but
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