local galaxy Trackster can't find bedtools

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3.5 years ago

j.matt.franklin • 0

Hi I'm running galaxy locally. I am trying to get the Trackster visualization tool to work.

The installation instructions are posted here: https://galaxyproject.org/visualization-setup/

When I attempt to run Trackster, I receive and error that bedtools cannot be found: PATH_TO_JOBS/tool_script.sh: line 9: bedtools: command not found

I have tried many ways to ensure that bedtools is on the correct path. For now, I have a symbolic link to bedtools in GALAXY_ROOT_DIRECTORY/.venv/bin

Also, bedtools is a package that can be installed from the toolshed. I installed that too and i'm still getting the error.

Does anyone know how I can ensure bedtools in on the right PATH?

software error RNA-Seq Galaxy • 674 views

ADD COMMENT • link updated 3.5 years ago by Biostar 20 • written 3.5 years ago by j.matt.franklin • 0

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Please post Galaxy related questions on their help forum for prompt response: https://help.galaxyproject.org/

ADD REPLY • link 3.5 years ago by GenoMax 142k

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