New subject: Dynamic data library

1 Oct 2013

      On 10/01/2013 03:53 PM, Cole, Nathan (NIH/NCI) [C] wrote:
...
Thank you both for your responses.  I will be looking into both of these.
With regard to the from_file option to add the sample selection into the tool:  I assume this means that the metadata and everything is loaded into galaxy at the time the tool is run.
This depends on how you write your tool. Do you just wanna read the ie 
fastq file or do you also wanna read the meta data. Also, how is the 
meta data accessible? eg. is it stored in a txt file at the same 
location as the fastq file?
...
Does this create a copy of the loaded file or simply read it in
place?  Also are there any efficiency issues created using this method, 
outside of the tool run time increase due to the load of the data taking 
place in-tool?
It should just read it in place
Hans-Rudolf
...
Thanks,
Nathan
-----Original Message-----
From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch]
Sent: Tuesday, October 01, 2013 4:07 AM
To: Cole, Nathan (NIH/NCI) [C]
Cc: Martin Čech; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Dynamic data library
Hi Nathan
Do you have many tools working with those samples or just a few? If you only have a limited, predefined set of tools you might wanna consider adding the sample selection into the tool.
You can use the from_file, or from_data_table options to dynamically create sample selection list. You can even drill down a hierarchical list. Have a look at ~/tools/annotation_profiler/annotation_profiler.xml
which uses the file
~/tool-data/annotation_profiler_options.xml
All you need to do is keeping the file in sync with the directory structure of your samples directory
Regards, Hans-Rudolf
On 09/30/2013 09:48 PM, Martin Čech wrote:
...
Hi Nathan,
Dannon answered similar question few days ago:
 There's an import mechanism in libraries that'll allow you to simply
 link to the file on disk without copy/upload.  I believe the
 "example_watch_folder.py" sample script (in the distribution) does
 just this via the API, if you want an example.

This might be what you are looking for.
Martin
On Mon, Sep 30, 2013 at 2:43 PM, Cole, Nathan (NIH/NCI) [C]
<nathan.cole@nih.gov mailto:nathan.cole@nih.gov> wrote:
 Hello, we’ve set up a local Galaxy instance in our genotyping and
 next-gen sequencing lab with local Apache LDAP (AD) integration, NFS
 mounts to a large NAS, and cluster integration coming.  Do to the
 high volume of samples and staff that will be using the system, I
 want to set up data libraries (without copying to Galaxy).  This is
 obviously no problem the first time, however I was wondering if
 there was a way to make a library, added from a system path, be
 dynamic so that it would stay synchronized with the underlying file
 structure?____

 __ __

 If a try dynamic library is not possible, is there a method for
 adding files to an existing library via that same system path that
 would not duplicate all of the original files in the data library?____

 __ __

 I did some scouring of the list and found some old unanswered
 questions and some things tangentially related topics, but I was
 unable to find a true answer or solution to my problem.  Any
 information on how to do the tasks above or other solutions to
 provide the same functionality would be greatly appreciated.____

 __ __

 Thanks,____

 Nathan____

 __ __

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