Question: This repository requires dependencies that cannot be installed through the Tool Shed
0
gravatar for testtoolshed
16 months ago by
testtoolshed30
testtoolshed30 wrote:

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?

ADD COMMENTlink modified 16 months ago • written 16 months ago by testtoolshed30

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

ADD REPLYlink written 16 months ago by Devon Ryan1.9k
1
gravatar for testtoolshed
16 months ago by
testtoolshed30
testtoolshed30 wrote:

Thank you, it's work now :)

ADD COMMENTlink written 16 months ago by testtoolshed30
0
gravatar for testtoolshed
16 months ago by
testtoolshed30
testtoolshed30 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 COMMENTlink written 16 months ago by testtoolshed30

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 REPLYlink written 16 months ago by Devon Ryan1.9k

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 REPLYlink written 16 months ago by Bjoern Gruening5.0k
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