Question: (Closed) Galaxy Tool Dependency
gravatar for gemayelkarl
5.7 years ago by
United States
gemayelkarl0 wrote:

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>
    <requirement type="package" version="1.2">theTool</requirement>
    tool_executable $input
    <param format="fasta" name="input" type="data" label="Source file"/>

<?xml version="1.0"?>
  <package name="theTool" version="1.2">
    <install version="1.0">
        <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>


​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 • 1.6k views
ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by gemayelkarl0

Hello gemayelkarl!

We believe that this post does not fit the main topic of this site.

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For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

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ADD REPLYlink written 5.7 years ago by RamRS30k
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