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,
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 
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?

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 


From: Jeremy Goecks []
Sent: Wednesday, September 25, 2013 8:43 AM
To: Curtis Hendrickson (Campus)
Cc:; Shantanu Pavgi (Campus)
Subject: Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff 

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.


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


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 - 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?


From: Jeremy Goecks []
Sent: Thursday, September 19, 2013 3:17 PM
To: Curtis Hendrickson (Campus)
Subject: Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff 

We can hack the old wrapper back in, using a hard-coded path to the old 

You could also use Managed Tool Dependencies for multiple versions of cuffdiff:

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.


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