Question: Have Galaxy install dependency for a custom tool
gravatar for chicken8duck
19 months ago by
chicken8duck0 wrote:


How do I install a dependency for a tool in galaxy.

I created the tool for galaxy. And simple placed it in the tools folder and changed the necessary files to recognize the tool.

This tool requires some additional libraries, that can be installed through pip.

How can I install these libraries?


galaxy • 400 views
ADD COMMENTlink modified 19 months ago by Martin Čech ♦♦ 4.9k • written 19 months ago by chicken8duck0
gravatar for Martin Čech
19 months ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

The best way to let Galaxy manage dependencies from dev and admins perspective is to use Conda package manager, see planemo docs for tool developer details regarding that matter.

To have Galaxy actually install the dependencies with the tool the tool itself needs to be in the Tool Shed and installed into Galaxy via the Admin interface by an administrator. The software dependency also has to be available in one of the default conda channels. Check the bioconda to see whether your dependencies are packed there.

That said if you pip install the dependencies on your machine instead and the system user that runs Galaxy has them on the $PATH Galaxy will find and run it when the tool needs it. However you are losing a lot of reproducibility and convenience for the user/admin.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Martin Čech ♦♦ 4.9k
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