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Question: Can Dependencies Be Handled in Custom Tools?
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gravatar for mccoykg
3.0 years ago by
mccoykg • 80
United States
mccoykg • 80 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 COMMENT • link •
modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by mccoykg • 80
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gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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. 

https://wiki.galaxyproject.org/ToolShed

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 3.0 years ago by mccoykg • 80
1

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 REPLY • link written 3.0 years ago by Martin Čech ♦♦ 4.9k

OK cool, I'll do that.

ADD REPLY • link written 3.0 years ago by mccoykg • 80
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