Hi Andreas, I've pushed a tiny fix to one patch so that wigeon runs - not sure why it was like that in the first place.
I'm not sure what was supposed to be happening with the symlinks but it makes sense to me that the individual packages install lower-case executables and the microbiomeutil package adds ChimeraSlayer,WigeoN,NAST-iEr to match the the names in the docs. I'm not sure what the shell wrapper script is up to, though. It just gives me an error: Expected '/usr/share/microbiomeutil/WigeoN' to be executable. /usr/bin/WigeoN: 11: exit: Illegal number: -1 I didn't write this script. Is it Steffen's? It seems like a complicated way to go about running three executables. Can't we just drop in three symlinks (/usr/bin/WigeoN -> wigeon) etc. and have done with it, do you think? Most of the Lintian warnings seem to be about the Changelog. You want to start at a pristine "-1" release while I want to preserve my history in Bio-Linux so I'm not sure what you want to do about that. Regarding UChime: There are several chimera detection methods and ChimeraSlayer is probably not the best of them, but it is still one that people use in standard protocols. UChime is actually in Debian as it currently sneaks in as a binary in the Mothur package. Normally you'd remove it from there and package the upstream source, but the authors of UChime say they will not be releasing any changes as they are committed to their non-free version. Mothur on the other hand is an active project with new releases so I'd say you're more likely to see fixes appearing in the Mothur source. So on this basis maybe uchime should be a separate package but it should still build out of the Mothur source. Does that make sense? Cheers, TIM On Tue, 2013-06-04 at 11:57 +0200, Andreas Tille wrote: > Hi Tim, > > On Mon, Jun 03, 2013 at 04:53:03PM +0100, Tim Booth wrote: > > This would be nice to get into Debian proper. Even though the upstream > > is not being updated the use of ChimeraSlayer seems to be important in > > many analysis protocols aside from being wanted by QIIME. > > BTW, I have found on their web page: > > Robert Edgar has developed a faster and more accurate chimera detection > tool called UCHIME. > (http://drive5.com/usearch/manual/uchime_algo.html) > > What about packaging this? > > > I think I'd failed to commit an important patch so have done that now, > > as well as trying to improve the long descriptions in the control file > > (though there's not much to say). > > Thanks. > > > A very minor thing - I notice the copyright file declares the packaging > > as GPL3+ while the main code is licensed under BSD. I habitually try > > not to add extra licenses if I can avoid it, so could we say the > > packaging files are simplified-BSD-licensed too? > > I changed this as suggested besides several other changes which IMHO > makes the packaging more smooth. > > Could you please have a look at the following: You had overriden > dh_install which made d/microbiomeutil.install ineffective. I changed > this which had the effect that some symlinks in the microbiomeutil > package now are not dangling any more but rather point to > /usr/bin/ChimeraSlayer. I'm not sure whether this is a wanted effect > or whether you want to ditch this script at all - at least it does > not show up in your binary package. > > It would be nice if you could do some general check whether I did > spoiled anything. I think I will try to work down the list of lintian > warnings a bit - lets see how far my time limit might reach. > > Any hints are welcome > > Andreas. > > -- > http://fam-tille.de > > -- Tim Booth <tbo...@ceh.ac.uk> NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/1370345925.6820.346.camel@balisaur
