On Feb 1, 2011, at 12:04 PM, Nicki Gray wrote:
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
>> 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
> 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?
Any user that uses the API will need an API key. They'll need to go to User ->
Preferences -> Manage your API keys to generate one if it is not set for them. The API
key only needs to be set once.
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
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?
The best approach for doing this would be to upload each new directory "version"
to a different folder or data library.
When you upload a directory of files, whether copying files into the Galaxy files location
or using file system paths, Galaxy creates pointers to those files, enabling the dataset
objects associated with them to be versioned.
Versions of local subdirectories cannot be done in Galaxy data libraries because the
structure of the data library hierarchy is "data library / folder / datasets",
and subdirectories themselves ( or information about them ) are not stored.
>> 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
What browser are you using? Safari, chrome or firefox are recommended as IE tends to have
many more behavioral problems like this.
Thanks for your help,
> Greg Von Kuster
>> Any help would be appreciated,
>> Thanks, Nicki
>> Nicki Gray
>> MRC Molecular Haematology Unit
>> 01865 222434
>> galaxy-dev mailing list
> Greg Von Kuster
> Galaxy Development Team
galaxy-dev mailing list
Greg Von Kuster
Galaxy Development Team