Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)
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
Reply to: