Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)
Hi Tin,
On Fri, Aug 12, 2016 at 03:30:25PM +0000, Duy Tin Truong wrote:
> > 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.
Sounds like a neat tool anyway - so if there is a description I could
provide a package.
> > > 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:
> https://bitbucket.org/biobakery/metaphlan2#markdown-header-metagenomic-strain-level-population-genomics
>
> and we may not change them again :).
So *if* you want to let users use the latest state of the repository why
don't you do a new versioned release to make it official. Debian uses a
system to check web pages for versioned releases. We can not sneak into
each repository nor wild guessing if it is a stable commit or not. Is
there any reason not to release say version 2.6 or 2.5.1 or whatever?
Kind regards
Andreas.
> > [1] https://bitbucket.org/nsegata/hclust2
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