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

[Andreas Tille]

Hi Michael,

On Thu, Feb 26, 2015 at 09:16:07PM +0000, Michael Crusoe wrote:
> > 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.
> >
> 
> Trimmomatic uses a nonstandard argument parser. "ILLUMINACLIP" is command
> line option, not an environmental variable. Adding `export
> ILLUMINACLIP=/usr/share/${ILLUMINACLIP}/adapters` to the wrapper script
> will have no effect.
> 
> Here is an example command line
> 
> TrimmomaticSE --phred33 input.fq.gz output.fq.gz
> ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3
> SLIDINGWINDOW:4:15 MINLEN:36

OK.  Would you mind having a look at

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

again?  Could you confirm that this package will close the bug and
provides what users expect?
 
> However no FASTQ format sequence files are provided in the package so I
> can't write a test case.

Well, we actually can add our own to debian/tests, can't we?

Kind regards

        Andreas.

-- 
http://fam-tille.de