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

[Dave Clements, GMOD Help Desk]

Hi Charles,

Note: I'm CC'ing Heng Li, the lead developer of SAMtools on this
thread.  The other two packages are part of GMOD.

Thanks for the information and the offer!

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?

Cheers,

Dave C.

On Thu, Nov 5, 2009 at 10:45 PM, Charles Plessy <plessy at debian.org> wrote:
> Le Thu, Nov 05, 2009 at 09:48:34AM -0800, Dave Clements, GMOD Help Desk a écrit :
>>
>> GBrowse NGS Tutorial
>>   http://gmod.org/wiki/GBrowse_NGS_Tutorial
>>   This step by step tutorial walks you through configuring GBrowse 2 to display
>>   data in SAMtools databases.  It includes a VMware image to work
>>   with, and uses the example human data that is included with SAMtools.
>
> Dear Dave,
>
> I noted that the VMware image is Debian or Ubuntu based. On Debian, the
> samtools, Bio::Graphics and Bio::DB::Sam packages are up-to-date in the
> unstable branch. We have a semi-official service to rebuild the packages from
> the unstable branch against the stable one, backports.org. Just let me know if
> you would be interested to list it in /etc/apt/sources.list so that the users
> would only have to use apt-get in order to grab the latest packages. For the
> moment I did not prepare backports, but would be happy to do so on demand.
>
> Have a nice day,
>
> --
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
>



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