Hi Greg
>>> 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?
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.
thanks, I will try this and see if this will do what we require and
let you know.
>
> 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?
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.
I was using Camino - I have just tried with Firefox and I can see all
the sub folders now.
Thanks for your help!
Nicki