[Debian-med-packaging] Fwd: Re: [j.johnson at imb.uq.edu.au: Re: Installation of binary tools inside MEME]

Wed Feb 27 16:07:43 UTC 2013

Hi Tim,

My only concern would be that we not create any conflict with the arrangement we have between the University of Washington, UC San Diego and the University of Queensland regarding The Meme Suite.  The technical compatibilities of the various versions are outside of my scope, but as long as we are not deviating from the agreement between our institutions, I have no issues with the request.

Thanks for copying me.

Dave

David G. Gibbons, PE, MBA
Assistant Director
Physical Sciences Licensing
Technology Transfer Office, UC San Diego
9500 Gilman Drive, MC 0910
La Jolla, CA 92093-0910
(858)534-0175
dgibbons at ucsd.edu
http://invent.ucsd.edu

From: Timothy Bailey [mailto:t.bailey at imb.uq.edu.au]
Sent: Wednesday, February 27, 2013 12:13 AM
To: James Johnson
Cc: Gibbons, David; Martin Frith; MEME Support; Debian Med Packaging Team
Subject: Re: Fwd: Re: [j.johnson at imb.uq.edu.au: Re: Installation of binary tools inside MEME]

James,
On 18/02/13 11:51 AM, James Johnson wrote:
Hi Tim, Dave,

The Debian Med Packaging Team want to know if they can backport GLAM2 improvements (presuming there are any?) in the MEME Suite to the more permissively licensed GLAM2 repository?
I have no problems with this as long as they do the work.

However, that will mean that the Debian version of Glam2 differs from the "standalone" version
Martin created.  It will match the "MEME Suite" version, though.

Cheers,

Tim

~James

-------- Original Message --------
Subject:

Re: [j.johnson at imb.uq.edu.au<mailto:j.johnson at imb.uq.edu.au>: Re: Installation of binary tools inside MEME]

Date:

Fri, 15 Feb 2013 11:04:58 +0000

From:

Tim Booth <avarus at fastmail.fm><mailto:avarus at fastmail.fm>

To:

Andreas Tille <andreas at fam-tille.de><mailto:andreas at fam-tille.de>

CC:

Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org><mailto:debian-med-packaging at lists.alioth.debian.org>, James Johnson <j.johnson at imb.uq.edu.au><mailto:j.johnson at imb.uq.edu.au>

Hi,

> On Thu, Feb 14, 2013 at 06:08:08PM +0000, Tim Booth wrote:

> > Yes, I did start looking at Meme but quickly realised it was a lot more

> > work than I thought to do a proper job on it.  I think all I wanted to

> > do in the first instance was to get an updated glam2 binary package

> > based upon the improved glam2 source within the meme code.  I guess this

> > is now the definitive glam2 as the original standalone source hasn't

> > been updated since 2008.

>

> We might try to do some comparison.  Charles previously mentioned that

> we should keep the glam2 package from Debian which is free (PD) and meme

> currently has a non-free license (according to DFSG).  So if glam2 inside

> meme is basically unchanged it might be reasonable to ignore the code

> inside meme (or asking upstream for permission to backport the changes.)

A quick "diff" across the original glam2 vs. the meme glam2 suggests

that several new options have been added for meme - see

src/glam2_args.c.

I would imagine that scripts within meme rely on these options.  In

fact, a quick grepping shows that scripts/glam2_webservice.pl.in calls

"glam2 -M" which is an option added for meme.  I've not looked for other

examples.

I hope that upstream can at least be persuaded to put their changes to

glam2 under a free license like the original glam2.  They may not be

legally bound to do so but it would be highly disingenuous  of them to

refuse.

Cheers,

TIM

--

If you can't find an apposite quote for your sig, just make one up.

     - Anon

--
Timothy L. Bailey

t.bailey at imb.uq.edu.au<mailto:t.bailey at imb.uq.edu.au>

Institute for Molecular Bioscience

VOICE: (61)-(7)-3346-2614

The University of Queensland

FAX: (61)-(7)-3346-2101

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http://research.imb.uq.edu.au/~tbailey<http://research.imb.uq.edu.au/%7Etbailey>

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