Matthias Dodt wrote:
Galaxy provides the upload of files from user directories via the
user_library_import_dir tag in universe_wsgi.ini.
There are two options: user_library_import_dir and library_import_dir.
Can you confirm that user_library_import_dir is the one you want?
library_import_dir should point to a directory which contains other
directories which can be selected (by administrators only) to upload the
user_library_import_dir should point to a directory which contains other
directories whose names match Galaxy user's email addresses. These
directories, in turn, contain directories which can be selected (by the
matching user) to upload the contents of.
1. If i choose "upload from directory" in the
data-libraries menu, first
i have a list of folders to choose. How can i assign different folders
to the same user? Normally it is only possible to upload files from the
users home directory, which matches the username i guess-
This feature was not designed with home directories in mind - it was
added so administrators could have a "drop box" type system: A per-user
FTP space or somewhere on disk, where each user could create their own
Note that symlinks are valid, so this is often an easy way to avoid
having to move too much data around.
2. There is an option: copy files into galaxy: yes/no. If i choose
it seems to me that the file gets copied still, because it takes ages to
There's metadata processing that also happens at this time. If you
select the file type manually (instead of leaving it as "automatic")
this should speed things up.
3. Assuming the "linking" of files into galaxy would work:
If i choose
once the users home directory for uploading files and link those into
galaxy, and later i add more files to the folder and want to upload
those, ALL files would be uplinked into galaxy again, no matter if they
already exist? Is there a way to choose which files of the folder should
There's not a simple way for Galaxy to know what files it has already
imported from a specific directory (or to know that you intentionally
did not want to upload duplicates).
This would probably be a good use for allow_library_path_paste, if
you're doing this as an administrator. allow_library_path_paste adds a
new upload page ("Upload files from filesystem paths") to the admin-side
library upload pages. This form contains a textarea that allows Galaxy
admins to paste any number of filesystem paths (files or directories)
from which Galaxy will import library datasets, saving the directory
structure (if desired).
Since such ability allows admins access to any file on the Galaxy server
which is readable by Galaxy's system user, this option is disabled by
default, and system administrators should take care in assigning Galaxy
administrators when this feature is enabled.
As with many of the security and library features, we have a certain way
of using them here at PSU, but are aware that other people use them
differently or need different features: if you have suggestions on how
we can make feature improvements, this helps us determine what direction
to go in the future.