Hi Shaun,

On Aug 1, 2012, at 6:13 AM, SHAUN WEBB wrote:

>>> c) The toolshed interface allows me to change the name of my tool. If I do 
>>> this, then go to my Galaxy admin ui and try to get updates for my tool then 
>>> it fails. Does it make sense to change a tools name after it is created? Is 
>>> it possible to track previous tool names to avoid this happening?
>> This should not occur.  Where are you able to change the name of your tool?  
>> You are not even allowed to change the name of the repository if it has been 
>> cloned (you can change the name of the repository as long as it has not been 
>> cloned).  Can you send me a screen shot of hte page that allows you to 
>> change the name of your tool in the tool shed?  I'll provide a fix as soon 
>> as I see where the issue lies.
> OK, I guess I changed the name of my repository not tool. I then installed 
> the tool via my local Galaxy instance. I can still change the name of the 
> repository in my toolshed and when I try to get updates via Galaxy admin 
> panel I get the following server error: "AttributeError: 'NoneType' object 
> has no attribute 'repo_path'"

I cannot reproduce this behavior, so can you let me know the steps you use to 
do so?  I need the page on which you are able to change the name of the tool 
shed repository in the tool shed after it has been cloned.  Here is a screen 
shot of what should be occurring after the repository is cloned.  Notice that 
the repository name is not alterable as it is no longer a text field.

Clone this repository:
hg clone http://g...@toolshed.g2.bx.psu.edu/repos/msjeon/abyss_tool
Repository names cannot be changed if the repository has been cloned.

>>> Running toolshed tools:
>>> I have no problems installing tools from toolsheds via Galaxy admin 
>>> interface, however I can't get these tools to run. They stay Grey forever 
>>> and look like this in the manage jobs table:
>>> 65  x...@xxxx.xx.ac.uk      0 minutes ago   
>>> toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_coveragebed_counts/0.1.0
>>>     new     None    None    None
>>> Do I have to set a tool runner or some other option for shed_tools?
>> No special configuration settings are required in your local Galaxy instance 
>> to to run tools installed from a tool shed.  If they stay in the queued 
>> state, there must be an issue in your local Galaxy instance that causes 
>> installed tools as well as tools included in the distribution to remain 
>> queued.  It has nothing to do with the fact they were installed.
> No. All other tools run fine. Tools installed from either my toolshed or the 
> Galaxy toolshed remain queued. If this is not a known issue then I will try 
> to dig a little deeper to find the problem. Any pointers would be useful if 
> you can think of why there should be a difference.

I've never seen this behavior before, and tools installed from the Galaxy main 
tool shed have been running on the main Galaxy server for some time.  No 
changes were made to the job components, so executing tools installed from tool 
sheds is no different in that regard from running tools included in the 
distribution.  It's difficult to tell you where to begin looking for the cause 
of the problem.

> Thanks for your help!
> Shaun
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

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