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Re: proteinortho does not find diamon(-aligner) executable

Hi Steffen,

in my mail I explained the reasons for the issue you stumbled upon and I
think from this you can obtain two ways for a solution easily (1. use
/usr/bin/diamond since its free now in diamond or 2. patch proteinortho
to use the Debian name).  Would you mind acting accordingly - preferably
after filing a bug where you document the issue?

Kind regards


On Fri, Dec 13, 2019 at 06:36:11AM +0100, Andreas Tille wrote:
> Hi Steffen,
> On Fri, Dec 13, 2019 at 12:33:26AM +0100, Steffen Möller wrote:
> > Hello,
> > 
> > I am just updating proteinortho and found that its tests look for a
> > series of binaries and executes the tests only if those binaries are in
> > the PATH. The diamond-aligner is a build package, likely for the reason
> > to be tested. The diamond-aligner's executable is also named
> > diamond-aligner - and not found.
> There was a package diamond inside Debian[1] and the name
> /usr/bin/diamond was occupied (documented in README.Debian of diamond).
> Since this was removed[2] the name is free again and we might consider
> taking over this name again.
> > Is this a bug of the diamond-aligner package to not offer some
> > compatibility layer or of proteinortho to use a non-standard executable
> > name? I'll team-upload proteinortho as it is now but something needs to
> > be done.
> If you suspect a bug why not filing one to make sure it will be found
> later?  I do not consider it the best idea to upload a known to be
> broken package.  You can contribute to our Advent bug squashing party
> by filing a bug find a solution and close it.
> Kind regards
>      Andreas.
> [1] https://tracker.debian.org/pkg/diamond
> [2] https://tracker.debian.org/news/1082936/removed-40515-5-from-unstable/
> -- 
> http://fam-tille.de


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