Question: tool_dependencies.xml Not Working - Why?
0
gravatar for mltaylor211
5 months 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.

tool dependency xml • 151 views
ADD COMMENTlink written 5 months ago by mltaylor2110
1
gravatar for Martin Čech
5 months ago by
Martin Čech ♦♦ 4.2k
United States
Martin Čech ♦♦ 4.2k wrote:

Have you had a look at the Conda package for Busco? https://bioconda.github.io/recipes/busco/README.html

If this is the software you want adding it as a dependency to your tool can be as easy as having <requirement type="package" version="3.0.1">busco</requirement> in the tool and removing the tool_dependencies.xml file.

The above assumes that you have conda-enabled Galaxy (which is every Galaxy release 17.01 or newer).

ADD COMMENTlink written 5 months ago by Martin Čech ♦♦ 4.2k
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