Hi Andreas, Yes, that is fine for me. Just a small comment, metaphlan2-data will depend on bowtie2 so that you can have bowtie2 to convert the fasta file. In addition, this is the list of dependencies for metaphlan2 in case you need: https://bitbucket.org/biobakery/metaphlan2#markdown-header-pre-requisites 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
Thanks, Tin On Fri, Aug 12, 2016 at 1:59 PM Andreas Tille <andr...@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 >
