The recommended installation is via the toolshed repository. Dependencies should be installed automatically when using Galaxy version >= 16.10.

The dependencies are dealt with Bioconda. To ensure that Bioconda is working check to make sure the following settings are in the config/galaxy.ini file:

# dependencies before each job runs.
conda_auto_install = True
# Set to True to instruct Galaxy to install Conda from the web automatically
# if it cannot find a local copy and conda_exec is not configured.
conda_auto_init = True