custom tool and text file

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Question: custom tool and text file

2.1 years ago by

snehalbpatil87 • 30

snehalbpatil87 • 30 wrote:

Hello everyone:

I am working on local instance of galaxy . My tool runs the bash script which needs the text file during execution. I want to avoid adding hard coded path to the file. Is there any way to keep the file in global location folder where tool can access it or do I need to hard code the path of that text file?

dependencies tool local custom • 618 views

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modified 2.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.1 years ago by snehalbpatil87 • 30

2.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Short answer: hard-coded

As far as I know, if a tool needs a specific external input that is not a dataset in the working history, then it needs to be included with the wrapped tool as a dependency. This would mean the file is included in the wrapper directly or it is in a distinct dependency package that is referenced by version. Even genome data referenced by tools (created by Data managers) have hard-coded paths to the file locations.

If someone else knows a way around this, please share.

Thanks, Jen, Galaxy

ADD COMMENT • link modified 2.1 years ago • written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

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