[med-svn] [poretools] 02/02: Initial packaging

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

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

commit 3d239002f8e81106c74f34d5a6fb6a8fc539c66c
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Nov 13 00:34:52 2015 -0800

    Initial packaging
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 31 +++++++++++++++++++++++++++++++
 debian/copyright         | 28 ++++++++++++++++++++++++++++
 debian/docs              |  1 +
 debian/rules             |  8 ++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             |  4 ++++
 9 files changed, 91 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..a6d18ee
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+poretools (0.5.1-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #nnnn)
+
+ -- Afif Elghraoui <afif at ghraoui.name>  Thu, 12 Nov 2015 23:44:42 -0800
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..18b7d64
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,31 @@
+Source: poretools
+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-h5py (>= 2.0.0),
+	python-rpy2 (>= 2.4.2),
+Standards-Version: 3.9.6
+Homepage: http://poretools.readthedocs.org
+Vcs-Git: git://anonscm.debian.org/debian-med/poretools.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/poretools.git
+
+Package: poretools
+Architecture: all
+Depends:
+	${misc:Depends},
+	${python:Depends},
+	python-pkg-resources
+Description: toolkit for working with nanopore nucleotide sequencing data
+ poretools is a flexible toolkit for exploring datasets generated by nanopore
+ sequencing devices from MinION for the purposes of quality control and
+ downstream analysis. Poretools operates directly on the native FAST5 (a
+ variant of the HDF5 standard) file format produced by ONT and provides a
+ wealth of format conversion utilities and data exploration and visualization
+ tools.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..4fc9db6
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,28 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: poretools
+Upstream-Contact: Aaron Quinlan <arq5x at virginia.edu>
+Source: https://github.com/arq5x/poretools
+
+Files: *
+Copyright: Aaron Quinlan <arq5x at virginia.edu>
+           Nick Loman
+License: TODO
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
+License: GPL-2+
+ This package 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 2 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 2 can be found in "/usr/share/common-licenses/GPL-2".
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..b43bf86
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.md
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..6454b3b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+
+include /usr/share/dpkg/default.mk
+
+%:
+	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/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..eeea94c
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Nicholas Loman and Aaron Quinlan
+  Title: "Poretools: a toolkit for analyzing nanopore sequence data"
+  Journal: Bioinformatics
+  Year: 2014
+  Volume: 30
+  Number: 23
+  Pages: 3399-3401
+  DOI: 10.1093/bioinformatics/btu555
+  PMID: 25143291
+  URL: http://bioinformatics.oxfordjournals.org/content/30/23/3399
+  eprint: http://bioinformatics.oxfordjournals.org/content/30/23/3399.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..e999939
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="filenamemangle=s/(?:.*?)?v?(\d[\d.]*)\.tar\.gz/poretools-$1.tar.gz/" \
+         https://github.com/arq5x/poretools/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz

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