On Thu, Feb 26, 2015 at 4:26 PM Andreas Tille <andr...@an3as.eu> wrote:
> 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? > The command I gave you was from their webpage; alas it contains two small errors: should be `-phred33` (single dash) and the adapter file needs to be a correct path; the file extension is missing. TrimmomaticSE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 This runs successfully on my system with local data. > > 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? > Right. I've tracked down the sequences they used in their paper but I can't find license nor copyright information: http://www.ebi.ac.uk/ena/data/view/SRX131047 While these files are rather large (113MiB) I could generate a subset for testing purposes. > > Kind regards > > Andreas. > > -- > http://fam-tille.de >