1:52 p.m.
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
/ <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(a)hpa.org.uk)
Bioinformatics, Centre for Infections, Health Protection Agency
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1:59 p.m.
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
/ <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(a)hpa.org.uk)
Bioinformatics, Centre for Infections, Health Protection Agency
-----------------------------------------
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The information contained in the EMail and any attachments is
confidential and intended solely and for the attention and use of
the named addressee(s). It may not be disclosed to any other person
without the express authority of the HPA, or the intended
recipient, or both. If you are not the intended recipient, you must
not disclose, copy, distribute or retain this message or any part
of it. This footnote also confirms that this EMail has been swept
for computer viruses, but please re-sweep any attachments before
opening or saving. HTTP://www.HPA.org.uk
**************************************************************************
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Paul-Michael Agapow