Re: Microbiomeutil and chimeraslayer as dependency of Qiime
Hi Andreas,
I spoke too soon on ChimeraSlayer. I've just run the test scripts
provided with QIIME and it is crashing because at some point it tries to
write to the /usr/share/microbiomeutil-data/RESOURCES directory.
It looks like this can be fixed by pre-computing some indices, by
running these two commands as root:
formatdb -p F -i /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta 2>/dev/null
cdbfasta -C /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta
So I guess these commands need to be added to postinst, with a
corresponding cleanup in postrm. Do you know where I can find an
example/template for doing this properly/robustly?
This also hilights that chimeraslayer needs to declare a direct
dependency on the blast2 package.
Cheers,
TIM
On Wed, 2013-06-05 at 09:25 +0100, Andreas Tille wrote:
> Hi,
>
> On Wed, Jun 05, 2013 at 08:34:14AM +0200, "Steffen Möller" wrote:
> >
> > microbiomeutil (20101212-2) unstable; urgency=low
>
> Done.
>
> > We all do not like working with epochs, I presume.
>
> I personally do not have a problem with epochs but I respect your
> feelings. :-)
>
> > I would also like to point
> > to the backports.debian.org page on packaging instructions
> > at http://backports.debian.org/Contribute/#index5h3
>
> Good hint. I was also wondering whether it is a good idea to use the
> "ubuntu" string inside BioLinux packages. As a (plain) Ubuntu user
> I would be a bit confused to see this name in the version if a package
> is not really part of Ubuntu but just an Ubuntu derivative. So if
> I were you and I would create versions for BioLinux most probably
> this would be the best idea for versioning:
>
> <version>~biolinux-<pkgversion> or
> <version>-0biolinux<pkgversion>
>
> A positive side effect is that people who stumbly by chance about such
> package will notice the BioLinux string and might become interested in
> it ...
>
> Kind regards
>
> Andreas.
>
--
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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