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.