[med-svn] [Git][med-team/metaphlan2][master] 6 commits: Rename package and source name from metaphlan2 to metaphlan

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / metaphlan2


Commits:
8b2f48d7 by Andreas Tille at 2022-08-04T17:14:39+02:00
Rename package and source name from metaphlan2 to metaphlan

- - - - -
0d656bf4 by Andreas Tille at 2022-08-04T17:15:17+02:00
New upstream version 3.1.0+renamed
- - - - -
6a8ae9a6 by Andreas Tille at 2022-08-04T17:15:17+02:00
Update upstream source from tag 'upstream/3.1.0+renamed'

Update to upstream version '3.1.0+renamed'
with Debian dir 89bca2fdd6cb50c0a06a3385ab679f38135bb250
- - - - -
05cb6cc3 by Andreas Tille at 2022-08-04T17:15:41+02:00
Fix typo

- - - - -
972027d7 by Andreas Tille at 2022-08-04T17:18:13+02:00
Simplify lintian-overrides

- - - - -
a4060609 by Andreas Tille at 2022-08-04T17:19:12+02:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/copyright
- debian/lintian-overrides
- debian/metaphlan2.1 → debian/metaphlan.1


Changes:

=====================================
debian/changelog
=====================================
@@ -1,8 +1,10 @@
-metaphlan2 (3.1.0-2) UNRELEASED; urgency=medium
+metaphlan (3.1.0+renamed-1) unstable; urgency=medium
 
   * d/watch: Create proper source tarball name
+  * Rename package and source name from metaphlan2 to metaphlan
+    Closes: #1016645
 
- -- Andreas Tille <tille at debian.org>  Thu, 04 Aug 2022 14:54:57 +0200
+ -- Andreas Tille <tille at debian.org>  Thu, 04 Aug 2022 17:18:25 +0200
 
 metaphlan2 (3.1.0-1) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -1,4 +1,4 @@
-Source: metaphlan2
+Source: metaphlan
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
@@ -13,10 +13,10 @@ Build-Depends: debhelper-compat (= 13),
 Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/metaphlan2
 Vcs-Git: https://salsa.debian.org/med-team/metaphlan2.git
-Homepage: https://bitbucket.org/biobakery/metaphlan2
+Homepage: https://github.com/biobakery/MetaPhlAn
 Rules-Requires-Root: no
 
-Package: metaphlan2
+Package: metaphlan
 Architecture: all
 Depends: ${python3:Depends},
          ${misc:Depends},
@@ -25,19 +25,20 @@ Depends: ${python3:Depends},
          python3-msgpack,
          python3-pandas,
          bowtie2
+Conflicts: metaphlan2
+Provides: metaphlan2
+Replaces: metaphlan2
 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.
+ microbial communities (Bacteria, Archaea and Eukaryotes) from
+ metagenomic shotgun sequencing data (i.e. not 16S) with species-level.
+ With the newly added StrainPhlAn module, it is now possible to perform
+ accurate strain-level microbial profiling.
  .
- MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes (the
- marker information file can be found at
- usr/share/metaphlan2/utils/markers_info.txt.bz2) identified from
- ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral,
- and ~110 eukaryotic), allowing:
+ MetaPhlAn relies on ~1.1M unique clade-specific marker genes (the latest
+ marker information file mpa_v31_CHOCOPhlAn_201901_marker_info.txt.bz2
+ can be found here) identified from ~100,000 reference genomes (~99,500
+ bacterial and archaeal and ~500 eukaryotic), allowing:
  .
   * unambiguous taxonomic assignments;
   * accurate estimation of organismal relative abundance;


=====================================
debian/copyright
=====================================
@@ -1,14 +1,14 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: MetaPhlAn2
+Upstream-Name: MetaPhlAn
 Upstream-Contact:  Nicola Segata <nicola.segata at unitn.it>
-Source: https://bitbucket.org/biobakery/metaphlan2/downloads
+Source: https://github.com/biobakery/MetaPhlAn
 
 Files: *
-Copyright: 2012-2018 Duy Tin Truong, Nicola Segata and Curtis Huttenhower
+Copyright: 2012-2022 Duy Tin Truong, Nicola Segata and Curtis Huttenhower
 License: expat
 
 Files: debian/*
-Copyright: 2016-2018 Andreas Tille <tille at debian.org>
+Copyright: 2016-2022 Andreas Tille <tille at debian.org>
 License: expat
 
 License: expat


=====================================
debian/lintian-overrides
=====================================
@@ -1,2 +1,2 @@
 # see https://lists.debian.org/debian-med/2018/06/msg00043.html
-metaphlan2: script-with-language-extension usr/bin/*.*
+metaphlan: script-with-language-extension


=====================================
debian/metaphlan2.1 → debian/metaphlan.1
=====================================



View it on GitLab: https://salsa.debian.org/med-team/metaphlan2/-/compare/a1dabe8b12efeb3f61151749d9c4774a2d51360d...a40606098a1bdf26f4222ccc02296c0b4c92a9fc

-- 
View it on GitLab: https://salsa.debian.org/med-team/metaphlan2/-/compare/a1dabe8b12efeb3f61151749d9c4774a2d51360d...a40606098a1bdf26f4222ccc02296c0b4c92a9fc
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