[med-svn] r22031 - in trunk/packages: . metaphlan2 metaphlan2/trunk metaphlan2/trunk/debian metaphlan2/trunk/debian/source metaphlan2/trunk/debian/upstream
Andreas Tille
tille at moszumanska.debian.org
Fri May 27 10:26:16 UTC 2016
Author: tille
Date: 2016-05-27 10:26:15 +0000 (Fri, 27 May 2016)
New Revision: 22031
Added:
trunk/packages/metaphlan2/
trunk/packages/metaphlan2/trunk/
trunk/packages/metaphlan2/trunk/debian/
trunk/packages/metaphlan2/trunk/debian/changelog
trunk/packages/metaphlan2/trunk/debian/compat
trunk/packages/metaphlan2/trunk/debian/control
trunk/packages/metaphlan2/trunk/debian/copyright
trunk/packages/metaphlan2/trunk/debian/rules
trunk/packages/metaphlan2/trunk/debian/source/
trunk/packages/metaphlan2/trunk/debian/source/format
trunk/packages/metaphlan2/trunk/debian/upstream/
trunk/packages/metaphlan2/trunk/debian/upstream/metadata
trunk/packages/metaphlan2/trunk/debian/watch
Log:
Very rudimentary packaging (leading to empty packages) but the metadata are there at least to point tasks pages to it
Added: trunk/packages/metaphlan2/trunk/debian/changelog
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/changelog (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/changelog 2016-05-27 10:26:15 UTC (rev 22031)
@@ -0,0 +1,5 @@
+metaphlan2 (2.5.0-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Mon, 23 May 2016 16:09:13 +0200
Added: trunk/packages/metaphlan2/trunk/debian/compat
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/compat (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/compat 2016-05-27 10:26:15 UTC (rev 22031)
@@ -0,0 +1 @@
+9
Added: trunk/packages/metaphlan2/trunk/debian/control
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/control (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/control 2016-05-27 10:26:15 UTC (rev 22031)
@@ -0,0 +1,37 @@
+Source: metaphlan2
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ python-all,
+ dh-python
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/metaphlan2/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/metaphlan2/trunk/
+Homepage: https://bitbucket.org/nsegata/metaphlan2/wiki/Home
+
+Package: metaphlan2
+Architecture: all
+Depends: ${python:Depends},
+ ${misc:Depends}
+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
Added: trunk/packages/metaphlan2/trunk/debian/copyright
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/copyright (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/copyright 2016-05-27 10:26:15 UTC (rev 22031)
@@ -0,0 +1,32 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: MetaPhlAn2
+Upstream-Contact: Nicola Segata <nicola.segata at unitn.it>
+Source: https://bitbucket.org/biobakery/metaphlan2/downloads
+
+Files: *
+Copyright: 2012-2016 Duy Tin Truong, Nicola Segata and Curtis Huttenhower
+License: expat
+
+Files: debian/*
+Copyright: © 2016 Andreas Tille <tille at debian.org>
+License: expat
+
+License: expat
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EV ENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR TH E USE OR OTHER DEALINGS IN THE SOFTWARE.
Added: trunk/packages/metaphlan2/trunk/debian/rules
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/rules (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/rules 2016-05-27 10:26:15 UTC (rev 22031)
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+
+%:
+ dh $@ --with python2
+
Property changes on: trunk/packages/metaphlan2/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/metaphlan2/trunk/debian/source/format
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/source/format (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/source/format 2016-05-27 10:26:15 UTC (rev 22031)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/metaphlan2/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/upstream/metadata (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/upstream/metadata 2016-05-27 10:26:15 UTC (rev 22031)
@@ -0,0 +1,11 @@
+Reference:
+ Author: Duy Tin Truong and Eric A Franzosa and Timothy L Tickle and Matthias Scholz and George Weingart and Edoardo Pasolli and Adrian Tett and Curtis Huttenhower and Nicola Segata
+ Title: "MetaPhlAn2 for enhanced metagenomic taxonomic profiling"
+ Journal: Nature Methods
+ Year: 2015
+ Volume: 12
+ Number: 10
+ Pages: 902–903
+ DOI: 10.1038/nmeth.3589
+ PMID: 26418763
+ URL: http://www.nature.com/nmeth/journal/v12/n10/full/nmeth.3589.html
Added: trunk/packages/metaphlan2/trunk/debian/watch
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/watch (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/watch 2016-05-27 10:26:15 UTC (rev 22031)
@@ -0,0 +1,3 @@
+version=3
+
+https://bitbucket.org/biobakery/metaphlan2/downloads .*/(\d\S*)\.tar\.gz
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