[Gmod-help] Re: [Gmod-gbrowse] GBrowse and NGS Data: Poster and Tutorial

[Charles Plessy]

Le Mon, Nov 09, 2009 at 03:43:56PM -0800, Dave Clements, GMOD Help Desk a écrit :
> 
> First, I think the current tutorial VMware image is probably fine as
> is, since it comes with SAMtools, Bio::Graphics, and Bio::DB::Sam
> already installed.  However, in the longer term anything that makes
> GBrowse installation easier is a very good thing.
> 
> If I understand your email correctly, these 3 packages could be
> automatically created and posted to the backports.org repository?
> Once that happens we could document on the GMOD web site (and maybe
> samtools.sourceforge.net for SAMtools?) that backports.org has these
> packages and we could include it in all future Debian/Ubuntu based
> GMOD tutorials.  Is that correct?
> 
> What would we have to do make that happen and to keep them current?
> Would we need to notify you whenever we release a new version?

Dear Dave and Heng,

The update of the packages in the backports.org repository is not automatic,
but each time I update SAMtools, Bio::Graphics, and Bio::DB::Sam in the Debian
development branch, I can update the backport to the stable branch as well.

I just realised that before I backport Bio::Graphics, I need to backport
BioPerl, which itself needs a backport of ExtUtils::Manifest. All in all, it
will take a couple of weeks to get everything done, because the first upload
is manually curated by volunteers, usually once per week, which makes this
step-by-step process a bit longer. Note that although it could work by accident,
the backports.org is not designed to supply packages to Ubuntu distributions.

Ubuntu has similar systems, the ‘Personnal Package Archives’ (PPA). If you know
some people intersted to maintain one, it would be my pleasure to provide some
guidance.

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan