Question: (Closed) Galaxy Tool Dependency
0
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>
  <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 • 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.

This question is better suited for https://biostar.usegalaxy.org/

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.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 5.7 years ago by RamRS30k
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