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:
>
> 1. 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
> / / 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.aga...@hpa.org.uk)
> Bioinformatics, Centre for Infections, Health Protection Agency
>
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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