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

[Michael Crusoe]

On Thu, Feb 26, 2015 at 3:13 PM Andreas Tille <andreas at an3as.eu> wrote:

> Hi Michael,
>
> thanks a lot for hints like these.  Do you think this is severity
> important or even serious (and thus we need to push the fix into
> Jessie)?  In the latter case we should stick to 0.32 otherwise I'd go
> with an update to latest upstream (0.33) which I just commited to SVN.
> (BTW, same here: If you intend to work on the package - I'm fine to
> move it to Git.  Just tell me.)
>

You are very welcome!

End users will expect adapter files to be installed and available. Please
push into Jessie.


> 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


>
> Thanks again
>
>     Andreas.
>
> --
> http://fam-tille.de
>
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