This can be done two ways:

(1) via sample tracking: http://wiki.g2.bx.psu.edu/Admin/Sample%20Tracking/Next%20Gen
(2) via the API; see the example script @ /scripts/api/example_watch_folder.py

Best,
J.

On May 23, 2012, at 5:00 PM, J. Greenbaum wrote:

Thanks for the reply.  Ideally, I would have a cron job run that would monitor a directory and automatically add the new files to a particular library.  I do not want the end users to have to deal with this.  Does anyone have a working solution or ideas for implementation?  This is the main sticking point that is preventing us from using galaxy for our in-house next-gen sequencing pipeline.

Thanks,

Jason

--
Jason Greenbaum, Ph.D.
Manager, Bioinformatics Core | jgbaum@liai.org
La Jolla Institute for Allergy and Immunology



From: "Alex Bossers" <Alex.Bossers@wur.nl>
To: "J. Greenbaum" <jgbaum@liai.org>, galaxy-dev@lists.bx.psu.edu
Sent: Wednesday, May 23, 2012 1:24:13 AM
Subject: RE: [galaxy-dev] upload from local filesysem

You can do so / allowing them to, by using the galaxy ftp solution.

That way users can link or provide files in their email subdirs. You have to sort out how to set the users/rights properly on your linux box though.

But see the galaxy ftp solution pages, it might be of help.

Alex

________________________________
Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens J. Greenbaum [jgbaum@liai.org]
Verzonden: woensdag 23 mei 2012 3:01
To: galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] upload from local filesysem

It seems that this topic has been covered at least several times and I've found this thread to be helpful:

http://user.list.galaxyproject.org/Speed-up-uploading-into-local-Galaxy-terribly-slow-tp4429327p4436053.html

However, as far as I understand, this will only allow the Admin to do the upload from a local disk.  Has anyone had success allowing a regular user to upload from a local disk?  This seems like a common issue, particularly with large sequencing files.  It would be great to be able to add this as the first step in a workflow.

Any info would be appreciated.

Thanks,

Jason

--
Jason Greenbaum, Ph.D.
Manager, Bioinformatics Core | jgbaum@liai.org<mailto:jgbaum@liai.org>
La Jolla Institute for Allergy and Immunology






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