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

On Tue, Feb 7, 2012 at 12:01 AM, Charles Plessy <plessy@debian.org> wrote:
> Le Mon, Feb 06, 2012 at 09:09:44AM -0500, Carlos Borroto a écrit :
>> I just notice that we are only recommending bowtie, but bowtie is
>> actually needed by tophat. All the actual mapping is done by bowtie. I
>> think we should have bowtie as a dependency of the binary package. I
>> have the commits ready for this, should I commit them and add an
>> UNRELEASED section to the changelog so we are ready for the next
>> upload?
> Hi Carlos,
> in general, do not hesitate to add an UNRELEASED section to the changelog and
> then commit changes to the repository.
> About the relation between tophat and bowtie, I indeed hesitated between
> Depends and Recommends, and chose Recommends as 1) it is installed by default
> anyway and 2) it would allow to install tophat independantly, which might
> be useful to some who want to use their own bowtie, or who want to use some
> of the helper tools in the tophat package.
> But if you think that Depends is better, go for it !

Hi Charles,

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.



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