Re: Status bowtie + tophat (Was: [Help] Need help for architecture specific code)
Hi,
I rephrase: Does anybody have a better idea to get tophat into testing
than simply restrict it to amd64?
Kind regards
Andreas.
On Sun, Aug 24, 2014 at 10:16:14PM +0200, Andreas Tille wrote:
> 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.
>
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