On 10/01/2013 07:12 PM, Cole, Nathan (NIH/NCI) [C] wrote:
One final question as I dive into looking at these two methods:  can you expose whole 
hierarchies and directories using the "from_file" method or will this only work 
on an individual sample basis?

yes, you can.
as an example have a look at the affymetrix cel files we offer. See attachment for a screen shot and the coresponding fragment from the xml file:

  <options>
      <option name="Affymetrix" value="Affymetrix">
<option name="HumanGeneST10_TissueData" value="HumanGeneST10_TissueData"> <option type="meta_key" name="MouseTP_Brain_01_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Brain_01_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Brain_02_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Brain_02_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Brain_03_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Brain_03_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Embryo_01_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Embryo_01_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Embryo_02_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Embryo_02_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Embryo_03_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Embryo_03_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Heart_01_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Heart_01_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Heart_02_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Heart_02_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Heart_03_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Heart_03_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Kidney_01_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Kidney_01_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Kidney_02_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Kidney_02_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Kidney_03_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Kidney_03_mGENE.CEL"/>
//
<option type="meta_key" name="MouseTP_Thymus_03_mGENE.CEL" value="/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Thymus_03_mGENE.CEL"/>
        </option>
<option name="MouseGeneST10_TissueData" value="MouseGeneST10_TissueData"> <option type="meta_key" name="MouseTP_Brain_01_mGENE.CEL" value="/***/***/external/Affymetrix/MouseGeneST10_TissueData/MouseTP_Brain_01_mGENE.CEL"/> <option type="meta_key" name="MouseTP_Brain_02_mGENE.CEL" value="/***/***/external/Affymetrix/MouseGeneST10_TissueData/MouseTP_Brain_02_mGENE.CEL"/>
//
<option type="meta_key" name="MouseTP_Thymus_03_mGENE.CEL" value="/***/***/external/Affymetrix/MouseGeneST10_TissueData/MouseTP_Thymus_03_mGENE.CEL"/>
        </option>
      </option>
      <option name="GEO" value="GEO">
//
      </option>
    </options>




If not, is there any method for exposing a the whole of a directory on the file 
system?

Thanks,
Nathan


-----Original Message-----
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Tuesday, October 01, 2013 10:11 AM
To: Cole, Nathan (NIH/NCI) [C]
Cc: 'galaxy-dev@lists.bx.psu.edu'
Subject: Re: [galaxy-dev] Dynamic data library



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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<<attachment: Screenshot-Affy-selection.png>>

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