[med-svn] [kineticstools] 02/03: Initial Packaging

Afif Elghraoui afif-guest at moszumanska.debian.org
Tue Dec 8 08:30:03 UTC 2015 

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afif-guest pushed a commit to branch master
in repository kineticstools.

commit 5fbf03bfb456a20aed411212f4b0e54335824d9e
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Mon Dec 7 23:00:09 2015 -0800

    Initial Packaging
---
 debian/changelog     |  5 +++++
 debian/compat        |  1 +
 debian/control       | 55 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/copyright     | 42 +++++++++++++++++++++++++++++++++++++++
 debian/docs          |  2 ++
 debian/rules         | 14 +++++++++++++
 debian/source/format |  1 +
 debian/watch         |  3 +++
 8 files changed, 123 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..51a3ded
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+kineticstools (0.5.1+20150828+git3aa3d96+dfsg-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #797676)
+
+ -- Afif Elghraoui <afif at ghraoui.name>  Thu, 29 Oct 2015 22:49:31 -0700
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..1b7c9cc
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,55 @@
+Source: kineticstools
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders:
+	Afif Elghraoui <afif at ghraoui.name>,
+Build-Depends:
+	debhelper (>= 9),
+	dh-python,
+	python-all,
+	python-setuptools,
+	python-pbcore (>= 1.2.2),
+	python-pbcommand (>= 0.2.0),
+	python-numpy (>= 1.6.0),
+	python-h5py (>= 1.3.0),
+	python-scipy (>= 0.9.0),
+Standards-Version: 3.9.6
+Homepage: https://github.com/PacificBiosciences/kineticsTools
+Vcs-Git: git://anonscm.debian.org/debian-med/kineticstools.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/kineticstools.git
+
+Package: kineticstools
+Architecture: all
+Depends:
+	${misc:Depends},
+	${python:Depends},
+	python-kineticstools (= ${source:Version}),
+	python-pkg-resources
+Description: detection of DNA modifications
+ Tools for detecting DNA modifications from single molecule, real-time (SMRT®)
+ sequencing data. This tool implements the P_ModificationDetection module in
+ SMRT® Portal, used by the RS_Modification_Detection and
+ RS_Modifications_and_Motif_Detection protocol. Researchers interested in
+ understanding or extending the modification detection algorithms can use these
+ tools as a starting point.
+ .
+ This package is part of the SMRTAnalysis suite.
+
+Package: python-kineticstools
+Section: python
+Architecture: any
+Depends:
+	${misc:Depends},
+	${shlibs:Depends},
+	${python:Depends},
+Description: detection of DNA modifications (Python 2 library)
+ Tools for detecting DNA modifications from single molecule, real-time (SMRT®)
+ sequencing data. This tool implements the P_ModificationDetection module in
+ SMRT® Portal, used by the RS_Modification_Detection and
+ RS_Modifications_and_Motif_Detection protocol. Researchers interested in
+ understanding or extending the modification detection algorithms can use these
+ tools as a starting point.
+ .
+ This package is part of the SMRTAnalysis suite and contains the backend
+ Python 2 library.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..4038cfa
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,42 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: kineticsTools
+Upstream-Contact: devnet at pacificbiosciences.com
+Source: https://github.com/PacificBiosciences/kineticsTools
+Files-Excluded: doc/whitepaper/*
+
+Files: *
+Copyright:
+	2011-2015 Pacific Biosciences of California, Inc.,
+	2012 Patrick Marks, David Alexander, Onureena Banerjee
+License: PacBio-BSD-3-Clause
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
+License: PacBio-BSD-3-Clause
+
+License: PacBio-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.
+ * Neither the name of Pacific Biosciences nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+ .
+ NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+ GRANTED BY THIS LICENSE.  THIS SOFTWARE IS PROVIDED BY PACIFIC
+ BIOSCIENCES AND ITS 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 PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS
+ 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/docs b/debian/docs
new file mode 100644
index 0000000..97d034d
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+README.md
+strand-conventions.txt
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..60801da
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+#include /usr/share/dpkg/default.mk
+
+export PYBUILD_NAME=kineticstools
+
+%:
+	LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
+
+override_dh_auto_install:
+	dh_auto_install
+	mkdir -p debian/kineticstools/usr/bin
+	mv debian/python-kineticstools/usr/bin/* debian/kineticstools/usr/bin
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/watch b/debian/watch
new file mode 100644
index 0000000..82ad58b
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+# Upstream has no release tags for us to watch.

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