However the hint ot hclust2[1] is helpful. Unfortunately I can not find
any description for this software. Since you might have some influence on
this it would be great to provide a hint where I can find a description for
a potential package.
hclust2 is used to plot heat-maps and not directly used in metaphlan2.py or strainphlan.py. In other words, metaphlan2 does not depend tightly on this tool. However, I will update the wiki page later.
> and here for strainphlan (another brother tool uses the same database with
> metaphlan2 and both are in the same repository and should go together,
> strainphlan is in strainphlan.py and metaphlan2 is in metaphlan2.py):
> https://bitbucket.org/biobakery/metaphlan2#markdown-header-pre-requisites_1
Well, the download file for metaphlan2 version 2.5 has strainer_src and
metaphlan2_strainer.py - is this what you mean?
Yes, strainer_src is now strainphlan_src and metaphlan2_strainer.py is now strainphlan.py. As I mentioned before, it is better to use the latest version of the repository now because the tutorial now fits with the new names:
and we may not change them again :).
Thanks,
Tin
Kind regards
Andreas.
[1] https://bitbucket.org/nsegata/hclust2
>
> On Fri, Aug 12, 2016 at 1:59 PM Andreas Tille <andreas@an3as.eu> wrote:
>
> > Hi Duy,
> >
> > On Thu, Aug 11, 2016 at 05:03:20AM +0000, Duy Tin Truong wrote:
> > > We have discussed the plan but unfortunately, we do not have enough
> > > resource for that task now. In addition, redesigning the source structure
> > > requires us to change all tutorials and that is quite expensive for us
> > and
> > > users now. We will inform you when we can separate them. Currently, the
> > > tutorial for users is here:
> > > https://bitbucket.org/biobakery/metaphlan2
> > >
> > > and fits well with latest version and it is quite stable now. We don't
> > > think that there will be a substantial update for the source code in the
> > > near feature.
> >
> > Thanks for the explanation which helps me to make a sensible decision.
> > I plan to do the following:
> >
> > 1. metaphlan2-data
> > The source tarball will be created by downloading the original
> > tarball from your site, strip the code and convert the data using
> > bowtie2-build markers.fasta ../db_v20/mpa_v20_m200
> > The Debian source tarball created this way will ship the fasta
> > version of the data and rebuilds the bowtie2 database at
> > installation time on users machine. I plan to enable the admin
> > to opt out from immediate generation and provide a script that
> > does the job later. I also plan to provide md5sums of the data
> > to ensure that the resulting database is really identical to the
> > metaphlan2 download.
> >
> > 2. metaphlan2 (the code):
> > The source tarball will be created by simply striping the data
> > and the binary Debian package as its done currently in my
> > packaging code. The metaphlan2 package will depend from the
> > metaphlan2-data package
> >
> > This does not require any change at your side but prevents over-large
> > packages on Debian site.
> >
> > Please confirm that this plan sounds sensible to you (or if I was not
> > explicite enough in my explanation).
> >
> > Kind regards
> >
> > Andreas.
> >
> > --
> > http://fam-tille.de
> >
--
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