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Bug#833388: marked as done (ITP: metaphlan2 -- Metagenomic Phylogenetic Analysis)

Your message dated Tue, 27 Sep 2016 12:00:29 +0000
with message-id <E1bor3l-0006LB-BO@franck.debian.org>
and subject line Bug#838083: fixed in metaphlan2 2.6.0+ds-1
has caused the Debian Bug report #838083,
regarding ITP: metaphlan2 -- Metagenomic Phylogenetic Analysis
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
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-- 
838083: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=838083
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>

* Package name    : metaphlan2
  Version         : 2.5.0
  Upstream Author : Nicola Segata <nicola.segata@unitn.it>
* URL             : https://bitbucket.org/nsegata/metaphlan2/wiki/Home
* License         : MIT
  Programming Lang: Python
  Description     : Metagenomic Phylogenetic Analysis
 MetaPhlAn is a computational tool for profiling the composition of
 microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from
 metagenomic shotgun sequencing data with species level resolution. From
 version 2.0, MetaPhlAn is also able to identify specific strains (in the
 not-so-frequent cases in which the sample contains a previously
 sequenced strains) and to track strains across samples for all species.
 .
 MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes (the
 marker information file can be found at src/utils/markers_info.txt.bz2
 or here) identified from ~17,000 reference genomes (~13,500 bacterial
 and archaeal, ~3,500 viral, and ~110 eukaryotic), allowing:
 .
  * unambiguous taxonomic assignments;
  * accurate estimation of organismal relative abundance;
  * species-level resolution for bacteria, archaea, eukaryotes and
    viruses;
  * strain identification and tracking
  * orders of magnitude speedups compared to existing methods.
  * metagenomic strain-level population genomics


Remark: The package is a target for Debian Med in itself and will be
used by metaBIT.  It will be maintained by the Debian Med team and the
packaging is currently available at
   svn://anonscm.debian.org/debian-med/trunk/packages/metaphlan2/trunk/


******* I'd like to discuss the following issue on debian-devel list *******

While Debian Med is injecting several low popularity contest packages
this one has an extraordinary large set of data and thus I want to
discuss the following options:

  1) Original orig.tar.gz has 1GB and contains 1.2GB uncompressed
     binary data.  License-wise it should not be a problem since
     there is a recipe given how to translate these into text form
     back and forth[1].

     We would have: source package 1GB + binary package 1GB

  2) When unpackaging the orig.tar.gz translating binary data to
     text format and recompress using xz the tarball is "only" 265MB.
     The transformation process takes about 30min on my Laptop - not
     longer than any larger project might need to build but the
     resulting binary package would have again close to 1GB.

     This enables the options:

     2a) Source tarball 256MB + binary package 1GB

     2b) Do the conversion of the format in postinst at the expense
         of users time which is acceptable since the package usually
         unpacks on high performance machines and not so many
         installations which means bandwidth and disk space on Debian
         mirrors should be saved here instead of users machine

         Source tarball 256MB + binary package ~250MB (estimated)

  3) Strip all data from the source package and download data in
     postinst from upstream Git repository.  This makes the package
     of uncritical size from a Debian point of view but might be
     problematic in some user setups which might have problems with
     larger data downloads (possibly be upstream can be convinced
     to provide a *.bz2 tarball for maximum compression).

     3a) Use postinst

     3b) Inform user to call a download script manually to do not
         block apt for a longer time dealing with potential download
         problems.

What do you think what strategy should be choosen to be kind to Debian
(and mirror) resources?

Kind regards

        Andreas.

[1] https://bitbucket.org/biobakery/metaphlan2#markdown-header-customizing-the-database

--- End Message ---
--- Begin Message --- 
Source: metaphlan2
Source-Version: 2.6.0+ds-1

We believe that the bug you reported is fixed in the latest version of
metaphlan2, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 838083@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated metaphlan2 package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Sat, 17 Sep 2016 12:26:03 +0200
Source: metaphlan2
Binary: metaphlan2
Architecture: source all
Version: 2.6.0+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 metaphlan2 - Metagenomic Phylogenetic Analysis
Closes: 838083
Changes:
 metaphlan2 (2.6.0+ds-1) unstable; urgency=medium
 .
   * Initial release (Closes: #838083)
Checksums-Sha1:
 8ed942c8a3e94fe4999d8a48f94a701bb6d3d8ba 2011 metaphlan2_2.6.0+ds-1.dsc
 fe49fbfeba7a45898838801f5b10c0d3814947a0 73312604 metaphlan2_2.6.0+ds.orig.tar.xz
 f22f00d1c18860976ed53d31f5e25f2f5a6d69bb 11560 metaphlan2_2.6.0+ds-1.debian.tar.xz
 a6755b65134ea33ae282ac17769fdd5b7188a3f8 73313228 metaphlan2_2.6.0+ds-1_all.deb
Checksums-Sha256:
 6f30dbc7c4ddd10f033d85f5c0d4c0e5473bafffb86f9b5fe6dd5b0f79011b22 2011 metaphlan2_2.6.0+ds-1.dsc
 a786948f93747dc6fe89a61e8c8102d15ec89d120b3280505509b66bfbb60d99 73312604 metaphlan2_2.6.0+ds.orig.tar.xz
 631f2c570103b720fefdcff7004985c022b4bd8231296d15b1edcd90a0a8d1b6 11560 metaphlan2_2.6.0+ds-1.debian.tar.xz
 36c4bcc9b0cb420771e799dd3391a73026028d8e8d247df79db254bd0ae66c3a 73313228 metaphlan2_2.6.0+ds-1_all.deb
Files:
 fe884d11271fa523a230abbd4f54118a 2011 science optional metaphlan2_2.6.0+ds-1.dsc
 babdd7521a871a9e94c02e80a75be2a2 73312604 science optional metaphlan2_2.6.0+ds.orig.tar.xz
 a01771ae29367e843d136754eb337bfb 11560 science optional metaphlan2_2.6.0+ds-1.debian.tar.xz
 6a3e8d7fcefa50a75e4dc32bdc8cc064 73313228 science optional metaphlan2_2.6.0+ds-1_all.deb

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--- End Message ---
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