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

Michael Crusoe michael.crusoe at gmail.com
Thu Feb 26 20:40:22 UTC 2015

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

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