Hi,
I develop a Galaxy tool that uses the R-package X. What is the recommended way of defining tool dependencies for my tool in Galaxy, so I can use the Tool Shed to distribute and deploy my tool?
Thanks,
Bjoern
Hi Björn ;)
You can use the setup_r_environment like we used here:
You can use this script with small modifications to create you such a file from scratch:
https://github.com/bioarchive/aRchive_source_code/blob/master/get_galaxy_tool_dependencies.py
At least to get started.
An other possibility is to use conda dependencies. So if your R package is already in conda/bioconda you don't need a tool_depenencies.xml file at all. Just specify in your tool requirement tag the conda package name and version and activate conda in Galaxy. This will do the trick. Conda dependency resolvers are available in Galaxy 16.01.
Ciao,
Bjoern
