Hi Ross, I think I need to clarify. I have a file in /home/galaxy/data-test/dir1/dir2/somefile.txt 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: /home/galaxy/galaxy-dist/database/files/000/data-test/dir1/dir2/dataset_id.dat. 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 directory? Thanks Neil ________________________________________ From: Ross [ross.lazarus@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, <Neil.Burdett@csiro.au<mailto:Neil.Burdett@csiro.au>> wrote: Hi, 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 Neil