[Bio-linux-dev] Problem with "mothur" in Bio-Linux 6

[Tim Booth]

Hi Tony,

I can't remember if there is a reason why UChime is missing, other than
just then nobody has got around to packaging it.  Mothur ships a copy of
the UChime source which is built by the build rules but then discarded.
Debian policy says that UChime should be packaged separately starting
from the main distribution tarball at
http://drive5.com/uchime/uchime_download.html (do you fancy having a go
if nobody else is working on it?).  Probably best to ask Andreas for
comments as he's the main packager - I'm copying him in.

Mothur goes to great lengths to look for the uchime binary in the same
location as the mothur binary.  This is annoying as it flies in the face
of Unix convention but it does mean that you can work around your
immediate problem by just symlinking mothur into /usr/local/bin.

Not looked into paths in uchime but I suspect it is just a matter of
changing the hard coded paths they use to the ones we use.

Cheers,

TIM

On Thu, 2012-03-01 at 00:15 +0000, Tony Travis wrote:
> Hi, Tim.
> 
> My colleague Rustam had a problem running "mothur" under Bio-Linux 6 
> recently. I had to kludge it to get it working because "uchime" was 
> missing and paths appear to be hard-coded in the "mothur" binary:
> 
> >[...]
> >> In the meantime, was trying to use chimera.slayer and chimera.uchime in
> >> Mothur but getting the error messages
> >>
> >> [ERROR]: /usr/bin/uchime file does not exist. mothur requires the uchime
> >> executable.
> >> [ERROR]: did not complete chimera.uchime.
> >
> > Hello, Rustam.
> >
> > I've installed "uchime" and created symbolic links on bobcat/topcat:
> >
> >   /usr/bin/uchime -> /usr/local/bin/uchime
> >
> > It seems that the paths are hard-coded in the "uchime" binary :-(
> >
> >> [ERROR]: /usr/bin/blast/bin/formatdb file does not exist. mothur
> >> requires formatdb.exe.
> >> [ERROR]: /usr/bin/blast/bin/blastall file does not exist. mothur
> >> requires blastall.exe.
> >> [ERROR]: /usr/bin/blast/bin/megablast file does not exist. mothur
> >> requires megablast.exe.
> >>
> >> If anything can be done about this? I do not have access to these
> >> directories to check.
> >
> > OK, I've kludged it so it will now work on bobcat/topcat:
> >
> >   /usr/bin/blast/bin -> /usr/bin
> 
> Can you tell me if any environment variables should be set to allow 
> "mothur" to use the conventional Bio-Linux 6 compatible paths?
> 
> I installed a separate version of "mothur" from source for QIIME.
> 
> Thanks,
> 
>    Tony.
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-- 
Tim Booth <tbooth at 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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