4.3 years ago by
United States
Hello,
Which to use has to do with the installation of complex tool dependencies, permitting customization of where tool (binary) installations and repository dependencies (other binaries, data types, etc.) are placed due to global variables included in the top level Galaxy configuration files. In short, these allow for controlling how common dependencies between tools are accessed (to avoid duplication) while also ensuring that specific required dependencies unique to a repo (due to version, binary compiling, and such) are placed to correctly to ensure expected/tested functionality. I'll share a few links that should help explain:
See the help for directing where to install a repository and dependencies (if any):
http://wiki.galaxyproject.org/ToolShedToolFeatures
This wiki demonstrate the actual usage in a Tool Shed Repo's tool (through an if/else statement):
http://galaxy-dist.readthedocs.org/en/latest/_modules/tool_shed/galaxy_install/tool_dependencies/common_util.html
For more like the above, the link below is a search function. It will bring up all references in our documentation and mailing list archives. Enter the variable names to find links like the ones above, plus much more. Combined with reviewing the top level config documents in the http://getgalaxy.org basic install, you'll get the bigger picture about usage options:
http://galaxyproject.org/search/getgalaxy/
The developers may add to this post, to refine, clarify, and even correct me where needed! Best, Jen, Galaxy team
