Hi all,

I am trying to install the Genome Diversity tools from the Miller Lab that are 
in the Galaxy toolshed.  I've been able to get all dependencies installed 
except Quicktree.  Whenever I try to install it, I get the error:

Error downloading from URL
<urlopen error ftp error: 550 pub4: No such file or directory>

This is the tool_dependencies.xml file for installing quicktree:

<?xml version="1.0"?>
  <package name="quicktree" version="1.1">
    <install version="1.0">
        <!-- Download source code -->
        <action type="download_by_url" 

        <!-- Build quicktree -->
        <action type="shell_command">make quicktree</action>

        <!-- Install quicktree -->
        <action type="shell_command">cp -R bin $INSTALL_DIR</action>

        <!-- Set environment for dependent repositories -->
        <action type="set_environment">
          <environment_variable name="PATH" 

I know this is not their file I'm downloading but the thing is, if I copy and 
paste the URL, I can download it with no problem.  I'm not sure why it's 
reporting that it can't be found but the xml looks right to me.  I've tried 
contacting the Miller Lab about this but haven't heard from anyone so I'm 
hoping someone here can tell me how to move past this problem.  Is there a way 
to install this tool manually and have the main Genome Diversity tools 
recognize it on the Galaxy server?

Also, I noticed when looking at the Tool Dependency Definitions at 
https://toolshed.g2.bx.psu.edu/ there are errors going back many versions for 
this tool (see Test runs - Installation errors - Tool dependencies).

Thank you for any help you can provide.


Dori Sajdak
Senior Systems Administrator
State University of NY at Buffalo
Center for Computational Research
701 Ellicott St
Buffalo, NY 14203
Phone: (716) 881-8934
Fax: (716) 849-6656
Web: http://ccr.buffalo.edu

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