Hi Tin, I need to admit that I can not parse the information you gave in your mail.
It is also not really connected to my next mail (which is archived here https://lists.debian.org/debian-med/2016/08/msg00040.html ) about the separation of code and data. Kind regards Andreas. On Thu, Aug 04, 2016 at 11:48:08AM +0000, Duy Tin Truong wrote: > Hi Andreas, > > If you can use the latest version with the name changes as I mentioned, it > would fit better with the updated tutorial on the metaphlan2 repository. > > Thanks, > Tin > > On Thu, Aug 4, 2016 at 1:28 PM Nicola Segata <[email protected]> wrote: > > > Hi Andreas, > > yes, it is likely that the code will be frequently updated, but the big > > database file will change only rarely (for sure no more frequently than > > once a year). > > thanks > > Nicola > > > > On Thu, Aug 4, 2016 at 12:46 PM Andreas Tille <[email protected]> wrote: > > > >> Hi again, > >> > >> On Thu, Aug 04, 2016 at 08:10:29AM +0000, Nicola Segata wrote: > >> > Makes sense to me! > >> > >> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=833388#15 > >> > >> If you read the discussion it seems that my suggestion to ship the fasta > >> file inside the Debian package and let the postinst do the > >> transformation step found some agreement - provided that there are no > >> frequent changes in the package and several uploads per month will > >> happen. > >> > >> I'm now wondering what your estimated change rate for the metaphlan2 > >> data files might be. Do these change frequently? Is there any chance > >> that the code changes frequently but the data files stay unchanged? > >> > >> Kind regards > >> > >> Andreas. > >> > >> > On Thu, Aug 4, 2016 at 8:18 AM Andreas Tille <[email protected]> wrote: > >> > > >> > > Hi Nicola, > >> > > > >> > > On Wed, Aug 03, 2016 at 08:51:33PM +0000, Nicola Segata wrote: > >> > > > Great, thanks Andreas. We provide the "*.bt2" files so that the > >> user can > >> > > > run BowTie2 internally to MetaPhlAn directly without first building > >> the > >> > > > indexes (it will take quite a bit of time). > >> > > > >> > > Fully agreed here. > >> > > > >> > > > Also, the indexes are smaller > >> > > > in size than the sequence file... > >> > > > >> > > Hmmm, all *.bt2 files sum up to 1,124,449kB while the fasta file has > >> > > only 753081kB. Considering the better compression performance of pure > >> > > text files a compressed archive containing the fasta is drastically > >> > > smaller than one with the *.bt2 files. Yesterday I tried to start a > >> > > discussion how to deal with the size of the data inside Debian[1] (no > >> > > answer so far) and my experiment to create a source tarball just > >> > > containing the fasta resulted in a 270MB *xz* compressed file (well xz > >> > > is better than gz but lets say the compressed tarball with the fasta > >> is > >> > > about 30% of size of your current download of 1.017MB. > >> > > > >> > > The situation for Debian is different than from your users: A user > >> who > >> > > downloads from your website intends to run metaphlan2. Amongst the > >> > > millions of Debian users only very few are interested in metaphlan2 > >> and > >> > > we need to outweight how much resources we could spent. Its not that > >> > > only Debian provides resources. There is a large mirroring network > >> that > >> > > spents lots of bandwidth and disk space for a very small usage. So in > >> > > this case it makes sense to put the effort on the users side to > >> > > regenerate the indexes (or even download the data separately via a > >> > > script we could provide inside the package). So I could imagine to > >> > > package only the metaphlan2 code and provide a script that downloads > >> the > >> > > data and puts them into the expected place. > >> > > > >> > > Kind regards > >> > > > >> > > Andreas. > >> > > > >> > > [1] > >> > > > >> https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-August/044984.html > >> > > > >> > > > cheers > >> > > > Nicola > >> > > > > >> > > > On Wed, Aug 3, 2016 at 6:08 PM Andreas Tille <[email protected]> > >> wrote: > >> > > > > >> > > > > Hi Tin, > >> > > > > > >> > > > > On Wed, Aug 03, 2016 at 02:01:01PM +0000, Duy Tin Truong wrote: > >> > > > > > > - Tin can also provide more info about the binary data in > >> db_v20. > >> > > The > >> > > > > files > >> > > > > > > ending with "bt2" are created using a script in the Bowtie2 > >> package > >> > > > > > > (bowtie2-build) using a sequence file Tin can provide (it can > >> also > >> > > be > >> > > > > > > recovered from the bt2 files with bowtie2-inspect if I > >> remember > >> > > well). > >> > > > > > As Nicola said, those files in db_v20 are created with > >> bowtie2-build > >> > > > > > using a sequence file and you can recover the sequence file by: > >> > > > > > > >> > > > > > bowtie2-inspect metaphlan2/db_v20/mpa_v20_m200 > > >> > > metaphlan2/markers.fasta > >> > > > > > > >> > > > > > If you want to rebuild them, the command is: > >> > > > > > > >> > > > > > bowtie2-build metaphlan2/markers.fasta > >> metaphlan2/db_v21/mpa_v21_m200 > >> > > > > > >> > > > > I can confirm that I can reproduce the files byte identical from > >> > > > > markers.fasta. Is there any reason to ship the binary form > >> instead of > >> > > > > the fasta text file? Moreover, what is the source of the > >> > > markers.fasta? > >> > > > > Is there any related publication or so? > >> > > > > > >> > > > > > > For the mpa_v20_m200.pkl Tin can also provide the uncompressed > >> > > python > >> > > > > > > object (or he can provide a couple of lines of code to > >> uncompress > >> > > it?) > >> > > > > > It is python dictionary and can be read as: > >> > > > > > > >> > > > > > import cPickle as pickleimport bz2 > >> > > > > > db = pickle.load(bz2.BZ2File('db_v20/mpa_v20_m200.pkl', 'r')) > >> > > > > > > >> > > > > > You can have more information about them at: > >> > > > > > > >> > > > > > >> > > > >> https://bitbucket.org/biobakery/metaphlan2#markdown-header-customizing-the-database > >> > > > > > >> > > > > OK, that page clarifies the method. Just a personal remark from > >> the > >> > > > > point of view of an outsider of bioinformatics: I'd regard the > >> > > creation > >> > > > > process of the mpa_v20_m200.pkl file a bit cumbersome. I'd > >> personally > >> > > > > prefer droping some text record somewhere and call a script > >> processing > >> > > > > this record rather than writing an own script. > >> > > > > > >> > > > > > In addition, some files were changed the names: > >> > > > > > - metaphlan2_strainer.py -> strainphlan.py > >> > > > > > - strainer_src -> strainphlan_src > >> > > > > > - strainer_tutorial -> strainphlan_tutorial > >> > > > > > > >> > > > > > Some source files were updated as well. > >> > > > > > Please let me know if you need other information. > >> > > > > > >> > > > > Just drop me a not once you might release a new version containing > >> > > these > >> > > > > changes. I think I'll try to release the current version as is > >> since > >> > > at > >> > > > > least the origin of the files is clarified now. I'm not yet sure > >> > > whether > >> > > > > the size of the data is acceptable or might spoil some limit. > >> > > Regarding > >> > > > > this I'm wondering whether I create a source tarball including > >> rather > >> > > > > markers.fasta and create the bt2 files in the build process. > >> > > > > > >> > > > > Kind regards > >> > > > > > >> > > > > Andreas. > >> > > > > > >> > > > > -- > >> > > > > http://fam-tille.de > >> > > > > > >> > > > >> > > -- > >> > > http://fam-tille.de > >> > > > >> > >> -- > >> http://fam-tille.de > >> > > -- http://fam-tille.de
