There's a bug in central and dist where a virtual environment defined as a tool dependency will fail to install packages via pip if the absolute path to the virtual environment `venv_directory` contains any spaces (i.e., a directory with a space in it exists on that path). I was able to fix the problem and have issued a pull request, but it looks like no one has looked at it yet: https://bitbucket.org/galaxy/galaxy-central/pull-request/195/allow-pip-to-ru... Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/