If you make the correction in your local version it should install.  However, 
getting updates (if they become available) may require merging.

On Mar 20, 2014, at 3:19 PM, Pete Schmitt <peter.r.schm...@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="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
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>>>  http://galaxyproject.org/search/mailinglists/
>> 
> 
> -- 
>  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
> 
> 
> <dartmouth.png>

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