Hi Andreas, Thanks for sorting the microbiomeutil stuff. It will be nice to see that getting into Debian, and I agree that UChime can wait until someone actually asks for it or until new OSS releases start appearing.
FYI, I'm working on the following in the next week or so: 1) Acacia - https://sourceforge.net/projects/acaciaerrorcorr/ Java app with the source now released (a month ago). Should be easy to do. 2) STADEN/Gap5 Been on the TODO list for ages but known to be awkward. I now have a volunteer tester plus a bunch of patches/hints to get it building so I'll get on with that and push progress to SVN. I can't recall if there is an ITP for that but I'll check. Cheers, TIM On Tue, 2013-06-04 at 14:51 +0200, Andreas Tille wrote: > Hi Tim, > > On Tue, Jun 04, 2013 at 12:38:45PM +0100, Tim Booth wrote: > > I've pushed a tiny fix to one patch so that wigeon runs - not sure why > > it was like that in the first place. > > Thanks for the quick check. > > > 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. > > OK, so symlinking the executables in the Dependant packages makes > sense to match the docs. I'll implement this. > > > 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? > > Most probably. > > > 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? > > Sure. I would have done this in the first place but I was not sure > about your opinion. > > > 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. > > I think I will ignore this one. I'd rather try to provide manpages > (perldoc unfortunately does not help but I tried some tricks with > help2man ... after removing some cruft with sed. No problem for a > project that is basically stalled, so we can go with manually edited > manpages). > > > 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. > > Ahh. Somehow I was comfortable with this name ... > > > 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? > > Well, if there is a real user base it might make sense. On the other > hand if it is non-free anyway we do have other interesting free projects > where we can kill our spare time with ... > > Thanks for your helpful comments > > 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/1370352831.6820.356.camel@balisaur
