Hi, when you specify a library_import_dir in universe_wsgi.ini with a path relative to galaxy-dist, i.e.

a directory: /home/galaxy/galaxy-dist/uploads is specified as: library_import_dir = uploads

and you then try to Upload directory of files, everything's reported as fine, but you end up with a 0 bytes file (which gives an error when trying to import it into any history). This is the case with Copy files into Galaxy selected.

If you instead try to Link to files without copying into Galaxy, the error is even more subtle because you can import the dataset into histories and even work with it, but auto-detection of the file format guesses the wrong datatype (just data for e.g. fasta format) and the dataset carries the message: Uploaded temporary file (path/filename) does not exist.

Everything's working just fine with an absolute path in universe_wsgi.ini, but I think the behaviour with relative paths is just bizarre. Apparently, some parts of Galaxy do use os.path.abspath, while others don't ?

My version of Galaxy is changeset 68a8b0397947 just in case this has recently been fixed.

Best, Wolfgang