I'm facing some issues when attempting to install a custom tool into galaxy. Here's my current setup:
- Created directory MyTool under tools/
- Created mytool.xml and tool_dependency.xml under tools/MyTool
The contents of the files are written below (I've simplified them slightly to make them shorter and easier to understand):
<tool id="mytool" name="My Tool"> <description> A tool </description> <requirements> <requirement type="package" version="1.2">theTool</requirement> </requirements> <command> tool_executable $input </command> <inputs> <param format="fasta" name="input" type="data" label="Source file"/> <inputs> </tool>
<?xml version="1.0"?> <tool_dependency> <package name="theTool" version="1.2"> <install version="1.0"> <actions> <action type="download_by_url">http://location-of-tool.tar.gz</action> <action type="move_directory_files"> <source_directory> . </source_directory> <destination_directory> $INSALL_DIR <destination_directory> </action> </actions> </install> </package> </tool_dependency>
My question now is, how do I get Galaxy to actually run the tool_dependency.xml file and download the tool? I can definitely get it to run the mytool.xml file, but can't seem to get it to download the tool using tool_dependency.xml. Am I missing something? I read the documentation many times but couldn't figure it out. Any help would be appreciated.