Re: [carlos.borroto@gmail.com: [SCM] tophat branch, oneiric-ppa, updated. oneiric-ppa/1.4.0-1_oneiric3-3-g3edf06d]

[Carlos Borroto <carlos.borroto@gmail.com>]

On Tue, Feb 7, 2012 at 6:10 PM, Charles Plessy <plessy@debian.org> wrote:
> Le Tue, Feb 07, 2012 at 10:14:20AM -0500, Carlos Borroto a écrit :
>>
>> I see your point but I think Depends is more appropriate. If someone
>> wants to use their own bowtie, I think they could still accomplish
>> that playing with $PATH. I also checked on the TopHat package from Tim
>> Booth at NEBC's PPA[1] and they are using Depends. I guess it would be
>> nice to keep the packages in sync for a future merge.
>>
>> BTW, the NEBC team is doing a very nice work packaging most of the
>> Tools a local install of Galaxy[2] would need. This is exactly what
>> got me interested in Debian packaging.
>>
>>  [1]https://launchpad.net/~nebc/+archive/galaxy
>> [2]htt[://galaxyproject.org
>
> Hi Carlos,
>
> it would be very exiting to see Galaxy packaged in Debian.
>

That would be great. For now I haven't even think about packaging
Galaxy itself, as I think it would be better to let Galaxy mature a
little more. There are many things drastically changing on Galaxy,
specially with the Tool Shed, that could mean a nightmare for a
maintainer.

> Please go ahead with Depends: bowtie.
>
> I see that you also added Recommends: cufflinks.  This is not possible as
> cufflinks is very unfortunately non-free.  Also, if nothing in the tophat
> package calls programs from the cufflinks package, the relationship would
> rather be that tophat Enhances: cufflinks and cufflinks Depends: tophat.
>
> Have a nice day,
>

Oh, I didn't realize adding something to Recommends implies it will
get installed by default just as a dependency. How can I get a
"Suggested packages: cufflinks" when apt-getting tophat? Is Enhances
mean for this?

I don't think tophat needs to be a Depends in cufflinks, as you could
be interested in the analysis of BAM files you didn't create or BAM
files not created with tophat. In order to run cufflinks you don't
need tophat at all. It could be a "suggestion"(Enhances?) thou, as
cufflinks authors do recommend mapping with tophat.

Regards,
Carlos