Hello Nik, I have put together a project that builds heavily on mi-deployment that does some of what you want to do (and probably a bunch of things you don't), but you could hopefully pull out just the parts you need. The idea behind the project is to build really cheap cloud galaxy instances by not using EBS or S3. From one simple command-line execution you can launch an instance, configure Galaxy, and transfer data into it (including optionally placing the data in a configured history). The command for doing this would be: ./run.sh --action=configure --action=transfer file1 file2 file3 The entire system is configure from one yaml file (including tools, genomes, and galaxy data (users, passwords, workflows, histories), etc...). See settings.yaml-sample for the myriad of options. This project is the driver, configure everything you need here and run the launch/configure/transfer script: https://bitbucket.org/jmchilton/galaxy-vm-launcher This project is a fork of galaxy-dist with changesets needed to implement this functionality: https://bitbucket.org/jmchilton/cloud-galaxy-dist So to prepopulate a history the way you described, you will want to define a user and create a history for that user by modifying the "galaxy" section of settings.yaml: galaxy: ## In order to create data libraries. First user should be admin@localhost ## and an API key must be specified, be sure to change API keys and passwords users: - username: admin@localhost password: adminpass api_key: 1234556789 - username: user1@example.com password: pass1 api_key: 987654321 ## Histories to create for this user histories: - TransferExampleHistory Then at the top-level of the yaml file you will need to specify the transferred data should be loaded into this history specified above: transfer_history_name: TransferExampleHistory transfer_history_api_key: 987654321 I think you will want to look at the seed_database function in lib/galaxy.py of galaxy-vm-launcher and the scripts/api/handle_uploads.py script in cloud-galaxy-dist. https://bitbucket.org/jmchilton/galaxy-vm-launcher/src/8ac4834dc08c/lib/gala... https://bitbucket.org/jmchilton/cloud-galaxy-dist/src/af9199b15195/scripts/a... Hope this is helpful, -John ------------------------------------------------ John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 On Tue, Jun 5, 2012 at 4:43 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:

Hi all,

I have a galaxy instance running in the Amazon Cloud that I have customized and I want to be able to transfer files (via scp) to the instance (or its attached storage) and then have those files show up automatically in the history.  Is this possible?  Alternatively, is there some way to automatically populate the history of a registered user, so that when that user logs in, the files are automatically in a saved history?  A third possibility would be to transfer the files and restart galaxy and then have the files show up automatically?  Just to be clear, I do not want to use the Upload Files tool at all.  Is there any way to implement any of these options?  Any help would be highly appreciated.  Thanks!

- Nik.

-- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client.  To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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