To answer my own questions, apparently I missed the
outputs_to_working_directory setting in config/galaxy.ini.
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden
> On 29 Dec 2015, at 14:04, Jorrit Boekel <jorrit.boe...@scilifelab.se&
to symlink files in (and how do I pass the working
dir in a tool XML)? I don’t want them in the files/ dir, looks bad, they’re not
cleaned, etc etc.
- Would it be a bad idea to make tools run inside a workdir, apart from
possibly breaking backwards compatibility?
cheers,
—
Jorrit Boekel
Proteomics
src’: ‘hda’,
‘id’: ‘abcdef12345’}} , history_id=‘abc1234’)
Is there any way to specify inputs_by in the payload or am I on the wrong
bioblend version? Otherwise I can file a request on the Bioblend github.
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockho
Thanks John, I found indeed the step order ids in the result from
export_workflow_json. Helps a lot and now I won’t need to use soon-deprecated
stuff.
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden
> On 19 Nov 2015, at 15:37, John Chil
and pushing this stuff. If there are smaller issues I can help with, I’d
be thrilled. Can’t stress enough how much this feature means for galaxy
adoption in our lab and possibly field.
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden
I thought the difference may be in the -central config handling that didn’t
work with my universe_wsgi anymore or something. Will be hard to trace so I
will leave this for now.
I'll mail you more about the collections though, probably tomorrow.
cheers,
—
Jorrit Boekel
Proteomics systems
as runtime triggered an error for me), due to the fact that the
workflow module type was not one of tool, data input, data collection, but was
instead the value of the type param which was currently filled in.
Now I know not to do this, hope you already did.
cheers,
—
Jorrit Boekel
Proteomics systems
