Question: tool_dependencies.xml Not Working - Why?
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mltaylor211 • 0 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.
