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:h...@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.c...@nih.gov <mailto:nathan.c...@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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