This repository requires dependencies that cannot be installed through the Tool Shed

Question: This repository requires dependencies that cannot be installed through the Tool Shed

22 months ago by

Hello, I am facing problem when I am trying to publish my new tool on tool shed. Everything work on my own instance but when I create public repository It's showing error:

This repository defines tool requirements that cannot be installed through the Tool Shed.Please activate Conda dependency resolution, activate Docker dependency resolution, setup Environment Modules or manually satisfy the dependencies listed below.

I don't understand why It cannot be installed through the Tool Shed and what I should do next. Could you please help me in this matter?

tool shed requires dependencies • 651 views

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modified 22 months ago • written 22 months ago by testtoolshed • 30

Which tool is this? One would need to see the requirements section.

ADD REPLY • link written 22 months ago by Devon Ryan • 1.9k

22 months ago by

testtoolshed • 30

testtoolshed • 30 wrote:

Thank you, it's work now :)

ADD COMMENT • link written 22 months ago by testtoolshed • 30

22 months ago by

testtoolshed • 30

testtoolshed • 30 wrote:

Hi, It's getGEO tool and his dependency repository methyldata1_16_2:

https://toolshed.g2.bx.psu.edu/view/testtool/get_geo/73cd17bea9c4 https://toolshed.g2.bx.psu.edu/view/testtool/methyldata_1_16_2/ea44a0861444

I have same issue with both of them and really short requirements section:

<requirements> <requirement name="methyldata_1_16_2" type="package" version="1.16.2">methyldata</requirement> </requirements>

ADD COMMENT • link written 22 months ago by testtoolshed • 30

I don't see a tool_dependencies.xml file anywhere. I suspect that if you uploaded one then this would be resolved. The following would probably work:

<?xml version='1.0' encoding='utf-8'?>
<tool_dependency>
    <package name="methyldata_1_16_2" version="1.16.2">
        <repository name="methyldata_1_16_2" owner="testtool" prior_installation_required="True" />
    </package>
</tool_dependency>

ADD REPLY • link written 22 months ago by Devon Ryan • 1.9k

The name attribute in your <requirement> is also not supported. You also might consider to put your dependency into BioConda and configure Galaxy to use them

ADD REPLY • link written 22 months ago by Bjoern Gruening ♦ 5.1k

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