Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)
Hi Duy,
thanks for the information. It might take some time since I'll be a bit
offline-ish next week but now I know what the correct target for the
package will be.
Kind regards
Andreas.
On Fri, Aug 19, 2016 at 07:17:25AM +0000, Duy Tin Truong wrote:
> Hi Andreas,
>
> Thanks for your explanation. We have officially updated metaphlan2 to
> version 2.6.0 as shown in tags.
> So, when it is convenient for you, please help to add the package of this
> new version.
>
> Many thanks,
> Tin
>
> On Fri, Aug 12, 2016 at 6:31 PM Andreas Tille <tille@debian.org> wrote:
>
> > 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
> >
> > --
> > http://fam-tille.de
> >
--
http://fam-tille.de
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