cp --parents does not appear to be doing what I though it would, trying mkdir instead.

  [localhost] local: sudo bash -c "cp --parents --recursive trinityrnaseq_r2012-10-05 /opt/galaxy/tools/trinity/r2012-10-05"
  cp: with --parents, the destination must be a directory
Galaxy: Improved support in bio_nextgen for Galaxy tool installs of tophat2 and bowtie2.
Galaxy: Change behavior of Galaxy tool installs so all installs are attempted and any errors and exceptions are reported and thrown at the end of the process. I am not sure why one would want to disable this, but the old behavior can be restored by setting galaxy_tool_defer_errors to False. Should we just simplify logic and disable this option?