Question: tool_dependencies.xml Not Working - Why?
0
gravatar for mltaylor211
2.5 years ago by
mltaylor2110 wrote:

I am working on writing a Galaxy tool that will run the genome assembly tool BUSCO. I have found that BUSCO has a few environment variables and path updates that need to be specified/exported before use. As such, I am trying to write a tool_dependencies.xml file to get this set up. It seems that what I have written so far has not been successful in exporting these environment variables.

Here is what I have written under the requirements tag in the XML file I wrote for my tool:

<tool id="g4" name="busco" version="0.0.2">
<requirements>
    <requirement type="package" version="3.0.1">BUSCO</requirement>
    <requirement type="set_environment">BUSCO_CONFIG_FILE</requirement>
    <requirement type="set_environment">AUGUSTUS_CONFIG_PATH</requirement>
</requirements>

Here is what I have written in my tool_dependencies.xml file:

<?xml version="1.0"?>
<tool_dependency>
    <environment_variable action="set_to" name="BUSCO_CONFIG_FILE">/opt/galaxy/galaxy-app/tools/busco/busco/config/config.ini</environment_variable>
    <environment_variable action="set_to" name="AUGUSTUS_CONFIG_PATH">/opt/galaxy/galaxy-app/tools/busco/augustus/config/</environment_variable>
    <package name="BUSCO" version="3.0.1">
        <actions>
            <action type="set_environment">
                <environment_variable action="prepend_to" name="PATH">/opt/galaxy/galaxy-app/tools/busco/augustus/bin/</environment_variable>
                <environment_variable action="prepend_to" name="PATH">/opt/galaxy/galaxy-app/tools/busco/augustus/scripts/</environment_variable>
            </action>
        </actions>
    </package>
</tool_dependency>

Any feedback or advice as to how I can improve my code would be greatly appreciated.

ADD COMMENTlink modified 2.3 years ago by martenson380 • written 2.5 years ago by mltaylor2110

You'll get a faster response to this on the galaxy site.

ADD REPLYlink written 2.5 years ago by Devon Ryan93k

Thank you, I will post the question there as well.

ADD REPLYlink written 2.5 years ago by mltaylor2110
1

Did you open this on the Galaxy Q&A site? Could you add the link here please.

ADD REPLYlink written 2.3 years ago by Peter5.8k
0
gravatar for martenson
2.3 years ago by
martenson380
PSU
martenson380 wrote:

BUSCO seems to be available in the bioconda channel of the conda package manager. Thus you can use it already in Galaxy and all you need is the proper <requirement> tag in your Galaxy tool wrapper.

There shouldn't be a need to make a Tool Shed package recipe for it, unless you need to use it on an older Galaxy.

ADD COMMENTlink written 2.3 years ago by martenson380
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