[Debian-med-packaging] Bug#779296: trimmomatic: directory of adapters missing from package

[Andreas Tille]

Hi Michael,

On Thu, Feb 26, 2015 at 08:40:22PM +0000, Michael Crusoe wrote:
> End users will expect adapter files to be installed and available. Please
> push into Jessie.

OK.  I'll bump the severity of this bug to serious.
 
> > Regarding the actual bug:  Do you have a clue to what directory in the
> > installed package the adapters need to be moved.  It seems they are
> > relative to the actual working dir and users are supposed to call the
> > package out of the source tree which is not possible.  Any hint about
> > the correct file system layout (if needed with patches) would be
> > welcome.  I'd like to fix this as soon as possible.
> >
> 
> The path to the specific adapter file to use is set by the user via the
> ILLUMINACLIP option, so the files can go into any directory;
> /usr/share/docs/trimmomatic/examples or /usr/share/trimmomatic come to mind
> 
> Their location should be highlighted in the manual pages and
> /usr/share/doc/README.Debian

Since we are using a wrapper anyway I have set this inside the wrapper
and thus do not see any need for README.Debian.  If you agree, please
have a look at

   https://people.debian.org/~tille/packages/trimmomatic/

and please test the package whether I have interpreted your links
correctly and the package can be uploaded as is.  If you could provide
a test using the adapters this would be more than welcome.  Our goal
should be tro get at least 80% of our packages autopkgtest-able.

Kind regards

      Andreas.

-- 
http://fam-tille.de