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.goecks@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:
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:
(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.