Hi Greg
thanks for your response, I have some questions about your reply.

On 1 Feb 2011, at 16:14, Greg Von Kuster wrote:
Hello Nicki,
On Jan 28, 2011, at 1:13 PM, Nicki Gray wrote:


As an admin I have created a data library on our local instance of galaxy, created folders in that library and added datasets using 'upload files from filesystem paths' option, choosing not to copy the data into Galaxy, which then loads all the files in the given directory into the data library.

Is there a way to refresh this list automatically? so that if a new file is added into that directory it will appear in the data library? or do I have to add new files in that directory manually, giving the path to the new file?

You could write a script that polls the desired directory and uses Galaxy's API to upload new files. See <galaxy install dir>/scripts/ api/README for some information. The distribution includes a script in this same directory to upload library datasets ( library_upload_from_import_dir.py ).

I have had a quick look at this script and I'm not sure this will do what we want. I see it says I should " browse to that user's preferences and generate a new API Key" - will it need to be done for each user?

What we would like is to initially upload a directory path for each user, and then the user can refresh this "library list" (or it happen automatically say, every 10 secs)

I notice that under the 'admin-manage data libraries' there is an 'Upload a new version of this dataset' option which replaces existing datasets - how easy would it be to create something similar for a directory? an "Upload a new version of this file system directory" and could the user be able to do that themselves?

I am also having a problem with creating sub folders - I choose to create sub folder from the drop down list and it reports that the sub folder has been created but I cant see it, and I cant click on the blue triangles to the left of the folders either. Does anyone else have this problem?

Assuming you are adding sub-folders from the Shared Data -> Data Libraries view ( and not the Admin - Manage data libraries view ), this may be a result of permissions that have been placed on the library or parent folder in which you are adding sub-folders. The behavior you see could be a bug, but if so, I'll need some help tracking it down. Can you confirm from what view you are adding hte sub-folders, and what the permissions are on the parent folder and library?

I was creating sub folders from the Admin - Manage data libraries view. I click on the arrow next the folder name, choose Add sub- folder, give it a name and get
"The new folder named 'xxx' has been added to the data library."
but I cant see it

Thanks for your help,


Greg Von Kuster

Any help would be appreciated,
Thanks, Nicki

Nicki Gray
MRC Molecular Haematology Unit
01865 222434

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Greg Von Kuster
Galaxy Development Team

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