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="shell_command">perl ./configureHomer.pl -install 
hg19</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.schm...@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
> 
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
> 
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to