[med-svn] [arden] 02/02: Initial raw Debian packaging
Andreas Tille
tille at debian.org
Fri Feb 7 12:00:07 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository arden.
commit 46a142dd5ff9c4724181530df3bff2d69e204af8
Author: Andreas Tille <tille at debian.org>
Date: Fri Feb 7 13:03:35 2014 +0100
Initial raw Debian packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 24 ++++++++++++++++++++++++
debian/copyright | 35 +++++++++++++++++++++++++++++++++++
debian/rules | 23 +++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream | 12 ++++++++++++
debian/watch | 5 +++++
8 files changed, 106 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..8436f68
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+arden (0.0.20130425-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Fri, 07 Feb 2014 11:38:38 +0100
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..0d95036
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: arden
+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)
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/arden.git
+Vcs-Git: git://anonscm.debian.org/debian-med/arden.git
+Homepage: http://sourceforge.net/projects/arden/
+
+Package: arden
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: specificity control for read alignments using an artificial reference
+ ARDEN (Artificial Reference Driven Estimation of false positives in NGS
+ data) is a novel benchmark that estimates error rates based on real
+ experimental reads and an additionally generated artificial reference
+ genome. It allows the computation of error rates specifically for a
+ dataset and the construction of a ROC-curve. Thereby, it can be used to
+ optimize parameters for read mappers, to select read mappers for a
+ specific problem or also to filter alignments based on quality
+ estimation.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..a379c44
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,35 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ARDEN
+Upstream-Contact: Sven H. Giese, gieses at rki.de
+Source: http://sourceforge.net/projects/arden/files/ARDEN/
+
+Files: *
+Copyright: 2012-2013, Sven H. Giese <gieses at rki.de>
+ Robert Koch-Institut
+License: BSDlike
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: BSDlike
+
+License: BSDlike
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ * The name of the author may not be used to endorse or promote products
+ derived from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL MARTIN S. LINDNER BE LIABLE FOR ANY
+ DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..58ec00b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,23 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables you can
+# include /usr/share/cdbs/1/rules/buildvars.mk
+# and use what is set there. Any hint whether dh might set variables in
+# a similar manner are welcome.
+
+%:
+ 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 b/debian/upstream
new file mode 100644
index 0000000..84f496f
--- /dev/null
+++ b/debian/upstream
@@ -0,0 +1,12 @@
+Reference:
+ Author: Sven H. Giese and Franziska Zickmann and Bernhard Y. Renard
+ Title: Specificity control for read alignments using an artificial reference genome-guided false discovery rate
+ Journal: Bioinformatics
+ Year: 2013
+ Volume: 30
+ Number: 1
+ Pages: 9-16
+ DOI: 10.1093/bioinformatics/btt255
+ PMID: 23685787
+ URL: http://bioinformatics.oxfordjournals.org/content/30/1/9
+ eprint: http://bioinformatics.oxfordjournals.org/content/30/1/9.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..5251033
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=3
+# unfortunately watch files does not work since upstream has no version numbers
+# see http://sourceforge.net/projects/arden/files/ARDEN/
+#
+# http://sf.net/arden/ARDEN-([0-9.]+)\.(?:tgz|tar\.gz|tar\.xz|tar\.bz2|zip)
--
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