The problem is likely a collision on the tool_id; update the tool ID for one of 
the wrappers and that should solve the problem.

Best,
J.

On Sep 24, 2013, at 5:30 PM, Curtis Hendrickson (Campus) wrote:

> Jeremy,
>  
> We didn’t have time to factor out to toolshed just now, so we took the 
> following approach
> 1.       Take 1.3-compatible cuffdiff wrapper (0.0.5) and move it to 
> cuffdiff_1.3_wrapper.py/xml – and add a dependency on cufflinks verson=1.3.0 
> (and set that up).
> 2.       Apply your patch, changing current cuffdiff wrapper to (0.0.6)
> 3.       Add a line in tool_conf.xml  so that both your modern cuffdiff v6 
> wrapper and our cuffdiff v5 wrappers are included.
>  
> When we restarted, and went to the GUI, there was only ONE cuffdiff tool 
> listed, and when you clicked on it, it brought up the 0.0.5 version (the 2nd 
> listed in tool_conf).
> There was no version pull down to get the 0.0.6 version.,
>  
> Any idea what I’ve missed?
>  
> Regards,
> Curtis
>  
>  
> From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] 
> Sent: Thursday, September 19, 2013 3:17 PM
> To: Curtis Hendrickson (Campus)
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff 
> version
>  
> We can hack the old wrapper back in, using a hard-coded path to the old 
> cuffdiff.
>  
> You could also use Managed Tool Dependencies for multiple versions of 
> cuffdiff:
>  
> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
> 
> 
> Shantanu suggests it might be a better world if we create a tool-shed 
> repository for the cuffdiff 1.3-2.1 (wrapper 0.0.5) version, then install 
> that.
> Would that be a better path, or just add confusion?
>  
> This is on the right path. The right thing to do is migrate the Cuff* tool 
> wrappers out of the galaxy-central/dist repositories; this is a bit more 
> effort than simply creating the tool-shed repository for the wrappers.
>  
> There are two reasons I haven't done this:
>  
> (a) time;
> (b) because the tools—and consequently the wrappers—are still in active 
> development, there needs to be a place for managing development of the 
> wrappers. Hence, the wrappers need a home on bitbucket or github, but we (the 
> Galaxy team) haven't determined where these wrappers should live.
>  
> (a) is a much more significant barrier than (b), so if a pull request 
> migrating Cuff* tools out of the distribution were made, I'm sure (b) could 
> be worked out.
>  
> Best,
> J.
>  

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