Galaxy Tool Dependency

Question: Galaxy Tool Dependency

3.8 years ago by

United States

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.

tool dependency galaxy xml • 1.2k views

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modified 3.8 years ago by Martin Čech ♦♦ 4.9k • written 3.8 years ago by gemayelkarl • 0

3.8 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

The correct filename is tool_dependencies.xml and it is used _only_ when the tool is being installed from the Tool Shed. You are adding your tool to your Galaxy manually thus you have to manually resolve its dependencies.

You can also create a toolshed repository at https://toolshed.g2.bx.psu.edu/ for your tool and then install it to your Galaxy through it using hte admin interface. During the process you will have an option to handle the tool dependencies automatically (based on the tool_dependencies.xml file).

ADD COMMENT • link modified 3.8 years ago • written 3.8 years ago by Martin Čech ♦♦ 4.9k

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