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Re: Microbiomeutil and chimeraslayer as dependency of Qiime



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


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