Hi Ross,
             I don't know of any tools that work in the way I want, but I'm not 
an expert on tools within Galaxy. Essentially the data in the directories will 
be fixed. We run a tool from Galaxy that generates some output data, this data 
then "checks" the data located under the directories I am trying to upload to 
Galaxy. There will probably be around 20 directories, and the data produced 
would then search these directories looking for "a closest match" once located 
it would use the remaining files in the directory to complete the process.

So for example, the application is segmenting an image, so a part of the image 
is the output. This is compared with files in the uploaded directories and a 
file in a particular directory is chosen (as the closest match) then the 
remaining files in the directory are then used to complete the process.

Does that make sense? There would be around 20 files in each directory.


From: Ross [mailto:ross.laza...@gmail.com]
Sent: Thursday, 3 January 2013 2:24 PM
To: Burdett, Neil (ICT Centre, Herston - RBWH)
Cc: galaxy-user
Subject: Re: [galaxy-user] Upload files from filesystem paths

It would help if you could point to an existing tool that works the way you 
want. I don't know of any that deal with arbitrary nested directories 
containing arbitrary files. A new composite datatype could impose a structure 
that a tool could be written to deal with (eg the pbed datatype used in some 
rgenetics tools) but arbitrary data structures are not going to be possible 
AFAIK. You're unlikely to get useful help without a much more complete and 
clear explanation of the problem.

On Thu, Jan 3, 2013 at 1:50 PM, 
<neil.burd...@csiro.au<mailto:neil.burd...@csiro.au>> wrote:
Hi Ross,
             I think I need to clarify. I have a file in 

Under the "Upload files from filesystem paths", In the "path to upload" window 
I paste "/home/galaxy/data-test". This then puts the "somefile.txt" in the 
/home/galaxy/galaxy-dist/database/files/000 directory. However, I elected to 
keep the directory structure. I can see this if I navigate through the "shared 
data" tab but where is this information stored under the galaxt-dist structure. 
As my application needs to have the directory structure kept, so need to access 
it from the xml/command line

I thought it might have been something like: 
But this is not the case rather  
/home/galaxy/galaxy-dist/database/files/000/dataset_id.dat. i.e. no directory 
structure. So how can I access this information from the xml files in the tools 

From: Ross [ross.laza...@gmail.com<mailto:ross.laza...@gmail.com>]
Sent: Wednesday, January 02, 2013 4:43 PM
To: Burdett, Neil (ICT Centre, Herston - RBWH)
Cc: galaxy-user
Subject: Re: [galaxy-user] Upload files from filesystem paths

Try importing those library files to the history where you want them - browse 
the Galaxy 'shared data' tab to where you uploaded them.

On Wed, Jan 2, 2013 at 11:39 AM, 
   I have a local galaxy installation.

I've created a data library, selected "Upload files from filesystem paths", 
pasted a path in the "path to upload" window, and I've selected to preserve the 
directory structure". And the files get imported.

How do I now access these files from my application? I don't want to import 
them into the history as then they lose the directory structure. I can't see 
where they are physically under the galaxy-dist structure

Thanks for any help


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:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


Reply via email to