> Jeremy,
>  
> I’m sure that would get both tools to show up, but it seems to me that would 
> miss the goal of past/future reproducibility.
>  
> My goal is to have to two versions of the program available at the same time –
> Cuffdiff_wrapper 0.0.5 (cuffdiff/links 1.3) the historical one that all the 
> current histories/workflows reference, so those don’t break,
> and
> Cuffdiff_wrapper 0.0.6 (cuffdiff/links 2.1) the new version for use going 
> forward, which has a distinct version so that those histories/workflows are 
> reproducible
> and the choice of which version to use is the users.
> I want to avoid someone who wants to re-run last-month’s cuffdiff with 
> slightly different parameters being forced (w/o their knowledge) to run a 
> more recent version of cuffdiff – which would then give an apples to oranges 
> comparison.
>  
> With 2 versions of the same ID installed, I expected to either see two 
> listings in the tool pane AND/OR a version pulldown on the cuffdiff tool 
> params pane.
>  
> Is the only way to get two versions of the same tool id installed via 
> toolshed?

Yes.

Unfortunately, it's not possible to manually install multiple versions of the 
same tool; the development efforts of the Galaxy team are focused on multiple 
version installation via only the tool shed for now. However, we'd welcome a 
pull request that adds this functionality to Galaxy.

Given that you want to provide backward compatibility, it's probably best to 
keep the tool_id for the older Cuffdiff wrapper and change the new one; 
mercurial merges should handle this change gracefully as it's small.

Best,
J.


>  
> Sorry – I feel like I’ve mis-understood the tool version/id resolution 
> architecture. Happy to talk on the phone if that would be a better use of 
> your time.
>  
> Thanks,
> Curtis
>  
>  
>  
> From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] 
> Sent: Wednesday, September 25, 2013 8:43 AM
> To: Curtis Hendrickson (Campus)
> Cc: galaxy-dev@lists.bx.psu.edu; Shantanu Pavgi (Campus)
> Subject: Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff 
> version
>  
> 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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