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

[Andreas Tille]

Hi Martin and Timothy,

many thanks for the clarification.  While I'm personally not glam or
meme user I would think that from a Debian packaging point of view it
would be quite reasonable to take over these changes fully to a glam2
package.  The rationale is that we would like to use the glam2 package
in connection with the MEME package and it would be simply confusing to
maintain two different glam2 packages while one is supporting MEME
options and one is not.

To approach this my idea would be as follows:  Fetch the glam2 files
straight from the MEME archive, create a tar archive containing glam2
exclusively and adapt the build process to build only the glam2
executables.  Build the Debian binary package glam2 from this source
archive.

Do you think this is a reasonable way to go and is it correct to keep
the old public domain license for this code.

Kind regards and many thanks for your cooperation

      Andreas.

On Thu, Feb 21, 2013 at 01:32:16AM +1000, Timothy Bailey wrote:
> Martin,
> 
> 
> On 19/02/13 8:56 PM, Martin Frith wrote:
> >Hi,
> >
> >I would approve of backporting those improvements with the more
> >permissive license.  But I didn't make most (any?) of them.  I
> >also believe the improvements are all cosmetic changes to the
> >interface, not changes to the algorithm.
> You are right about the nature of the changes.  Thanks for your
> understaning.
> 
> Cheers,
> 
> Tim
> >
> >Have a nice day,
> >Martin Frith
> >http://www.cbrc.jp/~martin/ <http://www.cbrc.jp/%7Emartin/>
> >
> >
> >
> >On Mon, Feb 18, 2013 at 10:51 AM, James Johnson
> ><j.johnson at imb.uq.edu.au <mailto:j.johnson at imb.uq.edu.au>> 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?
> >
> >    ~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  <http://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
> 

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