[med-svn] [centrifuge] 02/02: Initial packaging

Sat Nov 25 20:47:02 UTC 2017

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository centrifuge.

commit 42bbbd805e907653378e2779621b3c178ceaee99
Author: Andreas Tille <tille at debian.org>
Date:   Sat Nov 25 21:34:33 2017 +0100

    Initial packaging
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 27 +++++++++++++++++++++++++++
 debian/copyright         | 26 ++++++++++++++++++++++++++
 debian/rules             |  8 ++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             |  5 +++++
 8 files changed, 85 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..7ebf3cf
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+centrifuge (1.0.2~beta-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #xxx)
+
+ -- Andreas Tille <tille at debian.org>  Sat, 25 Nov 2017 21:24:23 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..9267ce3
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,27 @@
+Source: centrifuge
+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 (>= 10)
+Standards-Version: 4.1.1
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/centrifuge.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/centrifuge.git
+Homepage: https://ccb.jhu.edu/software/centrifuge/
+
+Package: centrifuge
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: rapid and memory-efficient system for classification of DNA sequences
+ Centrifuge is a very rapid and memory-efficient system for the
+ classification of DNA sequences from microbial samples, with better
+ sensitivity than and comparable accuracy to other leading systems. The
+ system uses a novel indexing scheme based on the Burrows-Wheeler
+ transform (BWT) and the Ferragina-Manzini (FM) index, optimized
+ specifically for the metagenomic classification problem. Centrifuge
+ requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial
+ genomes) yet provides very fast classification speed, allowing it to
+ process a typical DNA sequencing run within an hour. Together these
+ advances enable timely and accurate analysis of large metagenomics data
+ sets on conventional desktop computers.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..4cee6d8
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,26 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: centrifuge
+Upstream-Contact: centrifuge.metagenomics at gmail.com
+Source: https://github.com/infphilo/centrifuge/
+
+Files: *
+Copyright: 2013-2016 Daehwan Kim, Li Song, Florian P. Breitwieser and Steven L. Salzberg
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille at debian.org>
+License: GPL-3+
+
+License: GPL-3+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+ .
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+ .
+ On Debian systems you can find a copy of the full text of the  GNU General
+ Public License at /usr/share/common-licenses/GPL.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..f01a354
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+%:
+	dh $@
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..bed7398
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Daehwan Kim and Li Song and Florian P. Breitwieser and Steven L. Salzberg
+  Title: "Centrifuge: rapid and sensitive classification of metagenomic sequences"
+  Journal: Genome Research
+  Year: 2016
+  Volume: 26
+  Number: 12
+  Pages: 1721-1729
+  DOI: 10.1101/gr.210641.116
+  PMID: 27852649
+  URL: http://genome.cshlp.org/content/early/2016/11/16/gr.210641.116.abstract
+  eprint: http://genome.cshlp.org/content/early/2016/11/16/gr.210641.116.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..2857361
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=4
+
+opts="uversionmangle=s/-beta/~beta/" \
+  https://github.com//infphilo/centrifuge/releases .*/archive/v(\d[\d.beta-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/centrifuge.git

