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Re: Status bowtie + tophat (Was: [Help] Need help for architecture specific code)



Hi Charles,

On Sun, Aug 24, 2014 at 04:14:09PM +0900, Charles Plessy wrote:
> Le Sat, Aug 23, 2014 at 07:30:21PM +0200, Andreas Tille a écrit :
> > 
> > What can we do to get tophat and bowtie into testing?
> > 
> >  tophat:
> >     1. tophat only Recommends: bowtie2 | bowtie   or
> >     2. tophat Architecture: amd64 kfreebsd-amd64
> >  I think 1. is the better option
> 
> Hi Andreas,
> 
> In my understanding, it is not possible to run TopHat without Bowtie (version 1
> or 2).  Therefore, the “Depends” relationship is the most appropriate.
> 
> Regarding the migration to Testing, it looks like both bowtie2 and bowtie must
> be installable to satisfy “bowtie2 | bowtie”, so we need to adapt ourselves to
> this constraint.  Here are two possible solutions to the problem :
> 
>   1. bowtie2 and bowtie provide a virtual “bowtie-aligner”, and tophat
>      depends on “bowtie2 | bowtie-aligner”.
> 
>   2. tophat depends on bowtie2 only.

I do not think that this is necessary.  If tophat would be tophat

   Architecture: amd64 kfreebsd-amd64

it can migrate smoothly since the "Depends: bowtie2 | bowtie" is
perfectly fullfilled on these architectures.  The only thing is that
this means we give up in trying to build bowtie (1) on other than amd64
architectures.

> Given that bowtie and bowtie2 can be co-installed, and given that most users
> will want to use Bowtie 2 with TopHat, how about solution 2 ?

I'm fine with any solution which has tophat in Jessie on the practically
used architectures.  A bonus would be if it would work on all
architectures and as far as I understand people on debian-mentors the
amd64 optimisation code is overestimated but I guess we will not make it
without upstream and I do not remember that upstream mindet about any
response in this thread.

Kind regards

      Andreas.

-- 
http://fam-tille.de


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