[med-svn] [surankco] 02/03: Add initial packaging
Andreas Tille
tille at debian.org
Thu Mar 24 13:58:49 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository surankco.
commit b800535ae8c4802d32390a1ed2a4cbd50ede0629
Author: Andreas Tille <tille at debian.org>
Date: Thu Mar 24 14:49:10 2016 +0100
Add initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 21 +++++++++++++++++++++
debian/copyright | 34 ++++++++++++++++++++++++++++++++++
debian/rules | 22 ++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 4 ++++
8 files changed, 100 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..abec635
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+surankco (0.0.r5+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Thu, 24 Mar 2016 14:03:34 +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..e359b8d
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,21 @@
+Source: surankco
+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: 3.9.7
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/surankco.git
+Vcs-Git: https://anonscm.debian.org/debian-med/surankco.git
+Homepage: https://sourceforge.net/projects/surankco/
+
+Package: surankco
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: Supervised Ranking of Contigs in de novo Assemblies
+ SuRankCo is a machine learning based software to score and rank
+ contigs from de novo assemblies of next generation sequencing data. It
+ trains with alignments of contigs with known reference genomes and
+ predicts scores and ranking for contigs which have no related
+ reference genome yet.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..1aa6daf
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,34 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SuRankCo
+Source: https://sourceforge.net/projects/surankco/files
+Files-Excluded: *.jar
+
+Files: *
+Copyright: 2014-215 Mathias Kuhring <KuhringM at rki.de>, Robert Koch Institute, Germany,
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: BSD-3-clause
+
+License: BSD-3-clause
+ 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 Mathias Kuhring 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..1d11ebc
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/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/dpkg/default.mk
+# and use what is set there.
+
+%:
+ 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..f029154
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Mathias Kuhring and Piotr Wojtek Dabrowski and Vitor C. Piro and Andreas Nitsche and Bernhard Y. Renard
+ Title: "SuRankCo: supervised ranking of contigs in de novo assemblies"
+ Journal: BMC Bioinformatics
+ Year: 2015
+ Volume: 16
+ Number: 1
+ Pages: 240
+ DOI: 10.1186/s12859-015-0644-7
+ PMID: 26224355
+ URL: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0644-7
+ eprint: http://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0644-7?site=bmcbioinformatics.biomedcentral.com
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..d211c59
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,uversionmangle=s/^/0.0./,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ http://sf.net/surankco/surankco_(r[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
--
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