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 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
