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

[Michael Crusoe]

On Thu, Feb 26, 2015 at 4:01 PM Andreas Tille <andreas at 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
>
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