Jeremy,
Thanks for letting us know so quickly that we're heading down a non-viable path.
As I understand it, changing the tool id of the cuff* tools would solve our problem
locally, but make workflows created here non-interoperable with Galaxy Central.
We'll focus on moving to latest tool versions and educating uses on
non-reproducibility issues/work-arounds - probably providing the older wrappers under a
different tool_id, as your average user will want the latest one.
If we're blessed with some extra time, we'll tool-shed-ify it, but I can't
commit to that at the moment.
Thanks again for the super quick responses.
Regards,
Curtis
From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu]
Sent: Wednesday, September 25, 2013 10:43 AM
To: Curtis Hendrickson (Campus)
Cc: galaxy-dev(a)lists.bx.psu.edu; Shantanu Pavgi (Campus)
Subject: Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version
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.goecks@emory.edu]
Sent: Wednesday, September 25, 2013 8:43 AM
To: Curtis Hendrickson (Campus)
Cc: galaxy-dev@lists.bx.psu.edu<mailto: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.goecks@emory.edu]
Sent: Thursday, September 19, 2013 3:17 PM
To: Curtis Hendrickson (Campus)
Cc: galaxy-dev@lists.bx.psu.edu<mailto: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.