Re: Bug#794607: ITP: sortmerna -- tool for filtering, mapping and OTU-picking NGS reads
Hi Jenya,
thanks a lot for your super fast reply.
On Wed, Aug 05, 2015 at 07:44:41AM -0600, Jenya Kopylov wrote:
> Hi Andreas,
>
> I've uploaded the user manual 2.0 in tex format (see here
> <https://github.com/biocore/sortmerna>).
This is sufficient for the moment. Please make sure it will be included
into the downloadable tarball of your next release.
> Also, thank you for the man pages! I'll take a more thorough look later
> today.
Fine. I hope I did the formating sensibly enough.
> This month I plan to do a lot of updates to the overall code, so
> it's a good time to incorporate these.
:-)
> Let me know if you have other questions regarding the installation with
> QIIME.
May be I'll come up with more questions. We are currently working on
some remaining dependencies (sumatra and python-burrito-fillings).
> On Wed, Aug 5, 2015 at 7:23 AM, Jenya Kopylov <jenya.kopylov@gmail.com>
> wrote:
>
> > Thank you for reporting these issues,
> >
> > I will add the .tex file for the user manual 2.0 to github (SortMeRNA
> > development <https://github.com/biocore/sortmerna>).
> >
> > The latest QIIME release (1.9.1
> > <https://github.com/biocore/qiime/releases>) requires scikit-bio >=
> > 0.2.3, < 0.3.0 and SortMeRNA 2.0 (many of QIIME's scripts for 1.9.1 import
> > parse_fasta).
Ahhh, that's a pretty important hint. We might step back the Debian
version in this case most probably.
> > I can update the SortMeRNA tests to work with the latest
> > release of scikit-bio on the SortMeRNA development version, however they
> > will remain incompatible with QIIME 1.9.1 (and the development version)
> > since several other minor changes have been made (mainly the --blast
> > option) that will require additional changes in QIIME's tests.
> >
> > Greg, perhaps you can comment more on the scikit-bio release?
> >
> > Jenya
Thanks again for your very fast response
Andreas.
--
http://fam-tille.de
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