Re: Microbiomeutil and chimeraslayer as dependency of Qiime
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 <tbooth@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
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