Question: Can Dependencies Be Handled in Custom Tools?
gravatar for mccoykg
3.0 years ago by
United States
mccoykg80 wrote:

I've got several custom tools that are going to be published on the toolshed but are not currently. Right now they hard-code the paths to the tool dependencies, but I was wondering if there's a way to handle their dependencies with a tool_dependencies.xml like toolshed tools have? A colleague told me that tool dependencies can't be handled for tools that didn't come from a tool shed, but I wanted to double-check this.

dependencies custom tools • 621 views
ADD COMMENTlink modified 3.0 years ago by Jennifer Hillman Jackson25k • written 3.0 years ago by mccoykg80
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Any tool can have an associated tool_dependencies.xml file. This would be needed anyway before loading your new tools into the Tool Shed. (Not strictly required, but it is a better model to follow).

However, if the goal is to allow others to install the tool outside of a tool shed with managed dependencies, using the same mechanisms specific to those installed from a tool shed, then your colleague is correct.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k

Thanks! So what would be the correct mechanism for managing dependencies for tools outside of a toolshed / in the "tools" folder of an instance?

ADD REPLYlink written 3.0 years ago by mccoykg80

I am not sure there is a "correct" mechanism but you can just pretend in the wrapper.xml that everything is available to you (without absolute paths) and make sure that the dependencies are on job's PATH at runtime.

ADD REPLYlink written 3.0 years ago by Martin Čech ♦♦ 4.9k

OK cool, I'll do that.

ADD REPLYlink written 3.0 years ago by mccoykg80
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