[med-svn] [python-pbalign] 02/02: Initial Packaging

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
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commit ddc67d55d84b0a01f5b2e5caf2c59f9e652b51e9
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Tue Sep 1 20:10:16 2015 -0700

    Initial Packaging
---
 debian/changelog     |  5 +++++
 debian/compat        |  1 +
 debian/control       | 29 +++++++++++++++++++++++++++++
 debian/copyright     | 39 +++++++++++++++++++++++++++++++++++++++
 debian/docs          |  2 ++
 debian/rules         | 11 +++++++++++
 debian/source/format |  1 +
 debian/watch         |  2 ++
 8 files changed, 90 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..af92c9f
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+python-pbalign (0.2.0-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #797675)
+
+ -- Afif Elghraoui <afif at ghraoui.name>  Tue, 01 Sep 2015 19:24:27 -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..9d68938
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,29 @@
+Source: python-pbalign
+Section: python
+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 (>= 0.8.5)
+Standards-Version: 3.9.6
+Homepage: https://github.com/PacificBiosciences/pbalign
+Vcs-Git: git://anonscm.debian.org/debian-med/python-pbalign.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-pbalign.git
+
+Package: python-pbalign
+Architecture: all
+Depends: ${misc:Depends},
+	 ${python:Depends},
+	 blasr
+Recommends: python-pbh5tools,
+	    hdf5-tools
+Description: map Pacific Biosciences reads to reference DNA sequences
+ pbalign aligns PacBio reads to reference sequences, filters aligned
+ reads according to user-specific filtering criteria, and converts the
+ output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) 
+ format.
+ .
+ This package is part of the SMRTAnalysis suite.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..95d1943
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,39 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pbalign
+Upstream-Contact: Pacific Biosciences <devnet at pacificbiosciences.com>
+Source: https://github.com/PacificBiosciences/pbalign
+
+Files: *
+Copyright: 2011-2014 Pacific Biosciences of California, Inc.
+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:
+ 1. Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ 2. 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.
+ 3. 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..a826d35
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+LICENSES.txt
+README.md
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..0c8c1d6
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,11 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+export PYBUILD_NAME = pbalign
+
+%:
+	LC_ALL=C.UTF-8 dh $@ --with=python2 --buildsystem=pybuild
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..1279158
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+# Upstream (on github) has not tagged releases for us to watch
+#version=3

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