[med-svn] [spaced] 02/06: Add basic debian packaging files

Wed Mar 23 12:26:06 UTC 2016

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kloetzl-guest pushed a commit to branch master
in repository spaced.

commit 70121d6fe360ef55f809a5db548a594db8c02f19
Author: Fabian Klötzl <fabian at kloetzl.info>
Date:   Wed Mar 23 11:52:06 2016 +0100

    Add basic debian packaging files
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 29 +++++++++++++++++++++++++++++
 debian/copyright         | 29 +++++++++++++++++++++++++++++
 debian/rules             |  9 +++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             | 10 ++++++++++
 8 files changed, 96 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..332a2c5
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+spaced (1.0.2-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #81562)
+
+ -- Fabian Klötzl <kloetzl at evolbio.mpg.de>  `date -R`
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..18e7d3a
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,29 @@
+Source: spaced
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Fabian Klötzl <kloetzl at evolbio.mpg.de>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.7
+#Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/spaced/trunk/
+#Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/spaced/trunk/
+Homepage: http://spaced.gobics.de/
+
+Package: spaced
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: alignment-free sequence comparison using spaced words
+ Spaced (Words) is a new approach to alignment-free sequence
+ comparison. While most alignment-free algorithms compare the
+ word-composition of sequences, spaced uses a pattern of care and
+ don't care positions. The occurrence of a spaced word in a sequence
+ is then defined by the characters at the match positions only, while
+ the characters at the don't care positions are ignored. Instead of
+ comparing the frequencies of contiguous words in the input sequences,
+ this new approach compares the frequencies of the spaced words according
+ to the pre-defined pattern. An information-theoretic distance measure
+ is then used to define pairwise distances on the set of input sequences
+ based on their spaced-word frequencies. Systematic test runs on real and
+ simulated sequence sets have shown that, for phylogeny reconstruction,
+ this multiple-spaced-words approach is far superior to the classical
+ alignment-free approach based on contiguous word frequencies.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..ca40fcb
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: spaced
+Source: http://spaced.gobics.de/content/spaced-protein_dna.tar.gz
+
+Files: *
+Copyright: © 2015 Lars Hahn <lars.hahn at stud.uni-goettingen.de>
+License: GPL-3+
+
+Files: debian/*
+Copyright: © 2016 Fabian Klötzl <kloetzl at evolbio.mpg.de>
+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 package 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.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'. 
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..e8f077e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+	dh $@
+
+#get-orig-source:
+#	. debian/get-orig-source
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..1d2e596
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Burkhard Morgenstern and Bingyao Zhu and Sebastian Horwege and Chris-Andre Leimeister
+  Title: Estimating evolutionary distances between genomic sequences from spaced-words matches
+  Journal: Algorithms for Molecular Biology
+  Year: 2015
+  Volume: 10
+  Number: 1
+  Pages: 1-12
+  DOI: 10.1186/s13015-015-0032-x
+  PMID: 25685176
+  URL: http://dx.doi.org/10.1186/s13015-015-0032-x
+  eprint: http://almob.biomedcentral.com/track/pdf/10.1186/s13015-015-0032-x?site=almob.biomedcentral.com
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..dfe57a7
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,10 @@
+version=3
+
+http://spaced.gobics.de/ spaced-(.*)\.tar\.gz
+
+# if tweaking of source is needed
+# \
+# debian debian/get-orig-source
+
+# if you need to repack and choose +dfsg prefix
+# opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,compress=xz" \

-- 
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