bugs with relative path in library_import_dir

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

bugs with relative path in library_import_dir

Wolfgang Maier
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

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/