Hello Paul,
Assuming you have not configured your Galaxy instance to communicate with an external service ( e.g., a sequencer ), if you want to restrict access to the NGS files to a specific set of users, then your defined process is correct. If it is not important to restrict access to the data, then you can create public data libraries and your step 3 will not be necessary.
If your produced NGS data can be retrieved from a server that can communicate with your Galaxy instance, then you could potentially use a combination of Galaxy's Form Definitions and Sample Tracking ( available on the Admin menu ) to configure your Galaxy instance to communicate with the server to automatically retrieve the data and upload it to a data library, which can be created and configured with all necessary access permissions automatically. All of the Galaxy components currently exist to enable this, but there is no documentation on how to make it all work. Also, the UI for all of these components will be changing at some future time - there are plans for a Sample Tracking hack-a-thon at some point to re-work the UI. Due to these deficiencies, it may be best to not attempt to use this approach at the current time, but you can plan on this much more streamlined approach in the future.
Greg Von Kuster
On Aug 8, 2011, at 9:52 AM, Paul-Michael Agapow wrote:
So, I'm trying to setup a smooth pathway for our users to import their NGS data into Galaxy. I'd hoped for a solution that would require zero interaction with an administrator, but things seem more awkward than they should be:
- We can automagically push produced NGS data into a user import
directory on the host server. No problem. 2. The user can upload the data into via "Shared Data / Data Libraries / <name of data library> / Add datasets / Upload directory of files" 3. _But_ this data library must be created by an administrator, who must then assign appropriate permissions (access and add) for the appropriate user.
Have I got this right? I suppose that the last step only needs to be done once (create an "import library" for every users that I expect to want to import), but it seems a little fiddlier than expected. Is there an easier way, have I missed something?
Paul Agapow (paul-michael.agapow@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency
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