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
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
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
I was using Camino - I have just tried with Firefox and I can see all
the sub folders now.
Thanks for your help!
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