Re: Microbiomeutil and chimeraslayer as dependency of Qiime
Hi Tim,
many thanks for testing!
On Wed, Jun 05, 2013 at 12:27:36PM +0100, Tim Booth wrote:
> 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.
when I have read until this point I would have considered a patch to
write the output to /var/lib/microbiomeutil-data/RESOURCES or even move
the whole content to this place.
> 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
I simply trust your experience that this might bethe better solution.
> 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?
When it comes to templates I can only think of
/usr/share/debhelper/dh_make/debian
> This also hilights that chimeraslayer needs to declare a direct
> dependency on the blast2 package.
I'd suggest to wait until ftpmaster has accepted the package and
reupload then (or file a bug report if somethings stops us in
reuploading). I'm not a fan of redrawing and reuploading from / to new
queue because it creates extra manual work for ftpmaster which is
finally not needed if we fix the problem in SVN quickly and upload a fix
soonish.
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: