On Mar 20, 2014, at 3:19 PM, Pete Schmitt <Peter.R.Schmitt@dartmouth.edu> wrote:

Can I just edit this file to point to the existing homer install on the server? I found this in the tool shed tree.
On 3/20/14, 3:03 PM, Greg Von Kuster wrote:

Hi Pete,

Here is the recipe for installing homer from this repository:

http://toolshed.g2.bx.psu.edu/view/kevyin/homer

<?xml version="1.0"?>
<tool_dependency>
  <package name="homer" version="4.1">
    <install version="4.1">
      <actions>
        <action type="download_by_url">http://biowhat.ucsd.edu/homer/configureHomer.pl</action>
        <action type="shell_command">perl ./configureHomer.pl -install</action>
        
        <action type="move_directory_files">
          <source_directory>./</source_directory>
          <destination_directory>$INSTALL_DIR</destination_directory>
        </action>
        <action type="set_environment">
          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
        </action>
      </actions>
    </install>
    <readme>
      I'm sorry but this does not work

    </readme>
  </package>
</tool_dependency>

The problem is tha the following tag:

<install version="4.1">

must be:

<install version="1.0">

I'm pretty sure a message was displayed when the file was uploaded, but it's been a while since I looked at thie relevant code, so I'm not positive.

Gfreg Von Kuster

On Mar 20, 2014, at 2:52 PM, Pete Schmitt <Peter.R.Schmitt@dartmouth.edu> wrote:

I've installed homer 4.5 on the server that hosts the latest galaxy version, and ensured that
it is in galaxy's path (in run.sh) when it starts up. When installing the wrapper from the main toolshed
I get the following error which I don't understand:

Tool shed repository: homer

Tool shed repository changeset revision: f0b5827b6051

Tool dependency status: Error

Tool dependency installation error: Error installing tool dependency package homer version 4.1: Only install version 1.0 is currently supported (i.e., change your tag to be ).

Tool dependency installation directory: /galaxy/tools/homer/4.1/kevyin/homer/f0b5827b6051

The following is the README from the homer wrapper that I installed:

Homer wrapper for Galaxy

The homer tools will need to be accessible from command line

Code repo: https://bitbucket.org/gvl/homer

=========================================:
LICENSE for this wrapper:
=========================================:
Kevin Ying
Garvan Institute: http://www.garvan.org.au
GVL: https://genome.edu.au/wiki/GVL

http://opensource.org/licenses/mit-license.php

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Pete Schmitt Technical Director: Discovery Cluster NH INBRE Grid Computational Genetics Lab Institute for Quantitative Biomedical Sciences Dartmouth College, HB 6203 L12 Berry/Baker Library Hanover, NH 03755 Phone: 603-646-8109 http://discovery.dartmouth.edu http://columbia.dartmouth.edu/grid http://www.epistasis.org http://iQBS.org
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