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 >
