On Thu, Feb 26, 2015 at 4:01 PM Andreas Tille <andr...@an3as.eu> wrote:
> Hi Michael, > > On Thu, Feb 26, 2015 at 08:40:22PM +0000, Michael Crusoe wrote: > > End users will expect adapter files to be installed and available. Please > > push into Jessie. > > OK. I'll bump the severity of this bug to serious. > > > > 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 > > 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 However no FASTQ format sequence files are provided in the package so I can't write a test case. > Kind regards > > Andreas. > > -- > http://fam-tille.de >
