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

Andreas Tille andreas at an3as.eu
Thu Feb 26 22:45:28 UTC 2015

Hi Michael,

On Thu, Feb 26, 2015 at 09:41:35PM +0000, Michael Crusoe wrote:
> 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
> This runs successfully on my system with local data.

Thanks for checking.  I have uploaded to unstable and will file an
unblock bug tomorrow.  If anybody else could check the uploaded package
as well this would be cool.
> > 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.

I'm looking forward to this.

Kind regards



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