Re: Ping: Upgrading glam2 (Was: Installation of binary tools inside MEME)

[Charles Plessy <plessy@debian.org>]

Le Thu, Nov 14, 2013 at 04:59:21PM +0100, Andreas Tille a écrit :
> Ping,
> 
> I really need the help of testers for the new glam packages I uploaded
> for review here
> 
>    http://blends.debian.net/tmp/packages/glam2/
> 
> Any opinion would be very welcome.

Hi Andreas,

all of this is a lot of work, and we do not know for how long GLAM2 will be
disentanglable from the rest of the MEME source code.

I have used GLAM2 at the time I packaged it, but did not have opportunities
recently.  It is therefore hard for me to do serious tests.

Here are the entries relative to GLAM2 in MEME's changelog (slightly
reformated).

MEME version 4.4.0 -- April 23, 2010 

 * GLAM2: The output now prints a regular expression in addition to the logo
   for each motif found. 

MEME version 4.1.1 

 * Increased default number of iterations for GLAM2.

MEME version 4.0.0 -- June 13, 2008 

 * New web-based tools: GLAM2 and GLAM2SCAN--discovery and scanning of gapped
   motifs

 * Enhancements of existing tools: 
    -  Compare new motifs to databases of motifs via Tomtom by clicking an
       easy-to-use button on MEME and GLAM2 output.
    -  Hundreds of new genomic and upstream sequence databases are now
       supported for scanning by MAST, FIMO or GLAM2SCAN.

Since there is no critical improvement, I think that it is acceptable
to stay with the current glam2 package, and underline in the description
that this is not the version in MEME.

Then, if there are volunteers, a meme-glam2 package, conflicting with glam2 or
using the alternatives system, could be created and added in Debian's non-free
area.

Have a nice day,

-- 
Charles