Re: samtools 1.2 package layout change
On Fri, Aug 14, 2015 at 07:55:46AM +0900, Charles Plessy wrote:
> Le Thu, Aug 13, 2015 at 03:03:34PM +0100, Tim Booth a écrit :
> >
> > I was looking to see if it was worth pulling the samtools 1.2 package
> > into Bio-Linux (Ubuntu LTS Backports) and I can see that the package for
> > 1.2 has all the utility scripts going into /usr/bin where before they
> > were in /usr/{lib,share}/samtools. A slew of Lintian warnings results.
> >
> > I wondered if this is a deliberate change or just an artefact of the new
> > build system? I'd be happy to commit a fix that either restores the old
> > layout or else adds Lintian overrides. What do you think?
>
> Hi Tim,
>
> in the current 1.2 package, the scripts are installed in /usr/bin by the
> upstream build system, while before version 1.0 we installed them by hand in
> /usr/share, since they were not installed by the upstream build system.
>
> For the sake of compatibility with other distributions and platforms (that is,
> the rest of the World), I think that we should not remove the file extensions.
> Feel free to add a Lintian overrides. On my side, I am not doing so because
> overrides should be for false positives, while here it is the Policy that is
> plain wrong.
As an alternative we could move the files with extension to
/usr/lib/debian-med/bin
and link non-extension version to /usr/bin. How to set the PATH is
described in the plink package (where we had other reasons to move the
executable).
Kind regards
Andreas.
--
http://fam-tille.de
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