Tanguy LE CARROUR wrote:

Dear Nate!

On Wed, 2010-09-01 at 17:21 +0200, Tanguy Le Carrour wrote:

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On Wed, 2010-09-01 at 11:14 -0400, Nate Coraor wrote:

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This would be a great case for use of the (experimental) API. Set 'enable_api = True' in the config and then have a look at the README/scripts in scripts/api/

Thanks! It looks great! I'll test this. Unfortunately I've had no time those last weeks... months to play with Galaxy API! I've just downloaded the latest Galaxy version and I'm happily starting to test it! The Sample Tracking features are just great! Especially the "External services" importer which I planed to use to access our data repository.

But... after installing the rabbitMQ stuff (was it really necessary to rely on MQ?) I tried to import data and after one day it's still "In queue". There is no obvious error message in the logs... Is the feature still in testing or is it supposed to be production ready?

Hi Tanguy, It's under pretty heavy development and there are some major changes planned. Part of this will be dropping rabbitMQ (or at least the requirement for rabbitMQ - we will probably retain AMQP in the form of a slower python-based MQ that can be supplanted with rabbitMQ). That said, rabbitMQ should only be required for the barcode scanning functionality. For datast transfer, see the Transfer Manager and Deferred Job Runner, enabled with 'enable_beta_job_managers = True' in the config.

I would really love being able to use it... it would be even better with a "Link instead of copying"... but as it seems to use SCP I guess it's not possible!

Yes, you won't be able to link instead of copying using this method. It could be extended to do so but for now, it assumes it is copying data from a remote service.

Just to give you an overview of what we would like to do... We already have a project management system that also handles the raw data. We would need a workflow manager to work with the data (that are on the same drive). Somehow importing through the "Data Library" is a pain. With the external services the sample-file link is easy to create... but the data are copied!

I guess there would be a solution using the API but went I tried it it was still in beta phase.

It's still in beta but it should definitely do what you're trying to do. --nate

Any idea/advice welcome!

Thanks again for all your good work!

Best regards, Tanguy

-- Tanguy LE CARROUR

Functional Genomics Center Zurich ETH Zurich / University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland