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

Thu Feb 28 01:58:46 UTC 2013

James,

On 28/02/13 11:09 AM, James Johnson wrote:
> Hi Tim,
>
> On 28/02/13 11:05, Timothy Bailey wrote:
>> David,
>>
>> I assume the most important thing is that the copyright and "for 
>> non-profit use only"
>> warning is included in the Debian repackaging.  If those are 
>> preserved, I'm happy.
> If you refer to the original email, that's exactly what they were 
> hoping to avoid. GLAM2 has a more permissive license than the MEME 
> Suite. The reason they want to keep the 2 packages is so that people 
> can use GLAM2 under the more permissive license... They were hoping to 
> back-port any improvements to GLAM2 while keeping its original license.

Sorry about the confusion I may have called.  I am completely happy to 
have them
back-port changes from MEME Suite Glam2 to stand-alone Glam2.  The Glam2
license can remain as before.

My earlier comment referred to the Debian port of MEME Suite, not 
stand-alone Glam2.

Cheers,

Tim
>
> ~James
>>
>> Cheers,
>>
>> Tim
>> On 28/02/13 2:07 AM, Gibbons, David wrote:
>>>
>>> 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
>>>
>>> Brisbane, Qld. 4072 Australia
>>>
>>> 	
>>>
>>> http://research.imb.uq.edu.au/~tbailey 
>>> <http://research.imb.uq.edu.au/%7Etbailey>
>>>
>>
>> -- 
>> 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
>> Brisbane, Qld. 4072 Australia
>> 	http://research.imb.uq.edu.au/~tbailey
>>
>

-- 
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
Brisbane, Qld. 4072 Australia
	http://research.imb.uq.edu.au/~tbailey

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