[Debian-med-packaging] Bug#756780: Status bowtie + tophat (Was: [Help] Need help for architecture specific code)

[Charles Plessy]

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.

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 ?

Have a nice day,

-- 
Charles Plessy
Tsurumi, Kanagawa, Japan