Hi Andreas, > 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: https://bitbucket.org/biobakery/metaphlan2#markdown-header-metagenomic-strain-level-population-genomics 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 <[email protected]> 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 > > > > > -- > http://fam-tille.de >
