How to Use a Dependency in a Custom Tool

Question: How to Use a Dependency in a Custom Tool

3.4 years ago by

United States

mccoykg • 80 wrote:

Hi all. I've got a custom tool that relies on Biopython, and Biopython's installed under the "dependencies" folder. I've also got some lines in my code that try to tell Galaxy it needs to use Biopython (shown below) in my tool's xml file:

<requirements>
  <requirement type="package" version="1.65">biopython</requirement>
</requirements>

However, that doesn't seem to be enough to get the tool access to biopython. Biopython's documentation mentioned a file called "repository_dependencies.xml" that also needs to be edited, but that's for toolshed tools and not custom tools. I'm assuming I'm missing a parallel step required for custom tools, but I'm not sure what that would be. Thanks much.

dependencies • 1.1k views

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modified 3.4 years ago by Bjoern Gruening ♦ 5.1k • written 3.4 years ago by mccoykg • 80

3.4 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

You need to add a `tool_dependencies.xml` file into your package. For example this one: https://github.com/bgruening/galaxytools/blob/master/tools/augustus/tool_dependencies.xml but adjusted to biopython.

ADD COMMENT • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k

Thanks! I assume I'd be putting this in my myTools folder, right?

EDIT: I've tried this, and still get an error indicating that my tool can't find biopython. Currently my pathway to biopython is /home/galaxy/galaxy/dependencies/biopython, and my pathway to myTools which contains the tool dependent on biopython is /home/galaxy/galaxy/tools/myTools. I've put the tool_dependencies.xml file in the myTools folder and written it like so:

<?xml version="1.0"?>
<tool_dependency>
    <package name="myTools">
        <repository name="biopython"/>
    </package>
</tool_dependency>

ADD REPLY • link modified 3.4 years ago • written 3.4 years ago by mccoykg • 80

You need to specify the 'owner' as well. Please try to mimic the example above.

ADD REPLY • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k

I'll add that in. What would the owner be, my username when using galaxy?

ADD REPLY • link written 3.4 years ago by mccoykg • 80

According to: https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_65/ the owner is biopython. This is a ToolShed group maintaining this package.

ADD REPLY • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k

I've fixed up the tool_dependencies.xml file, but my tool still can't find biopython. Right now it reads:

<?xml version="1.0"?>
<tool_dependency>
<package name="myTools">
<repository name="package_biopython_1_61" owner="biopython"/>
</package>
</tool_dependency>

Is there anything else that could be wrong with this?

ADD REPLY • link written 3.3 years ago by mccoykg • 80

Can you point me to your entire tool? Is is on github/bitbucket?

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

It's not available online anywhere yet for security reasons; I'll try to list out the relevant pathways if that will help. Thanks for being so patient with this.

The custom tool is called calc_fitness.py and its corresponding xml file is calc_fitness.xml. It, along with other custom tools, are located in /home/galaxy/galaxy/tools/myTools. calc_fitness.py relies on biopython in that it uses the SeqIO module.

My tool_dependencies.xml file is also located in the myTools folder, and is written as I posted just above.

I have biopython version 1.61 located under /home/galaxy/galaxy/dependencies/biopython and called "1.61".

I hope that's helpful! Sorry it's not on github.

ADD REPLY • link written 3.3 years ago by mccoykg • 80

can you send it to me privately ...

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

I'm afraid I can't... however, my server admin may have figured out a work-around where he installs biopython, so I think we're good. Thanks for all your help.

ADD REPLY • link written 3.3 years ago by mccoykg • 80

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