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

Fri Sep 1 13:01:58 UTC 2017

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tille pushed a commit to branch master
in repository nanook.

commit dc656cb0ac604aa039cccac469da9e161a59c61b
Author: Andreas Tille <tille at debian.org>
Date:   Fri Sep 1 15:01:09 2017 +0200

    Initial packaging
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 27 +++++++++++++++++++++++++++
 debian/copyright         | 27 +++++++++++++++++++++++++++
 debian/rules             | 22 ++++++++++++++++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             |  4 ++++
 8 files changed, 99 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..a1a5488
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+nanook (1.26+dfsg-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Fri, 01 Sep 2017 14:39:50 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..603be74
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,27 @@
+Source: nanook
+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 (>= 10)
+Standards-Version: 4.1.0
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/nanook.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/nanook.git
+Homepage: https://documentation.tgac.ac.uk/display/NANOOK/NanoOK
+
+Package: nanook
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: pre- and post-alignment analysis of nanopore sequencing data
+ NanoOK is a flexible, multi-reference software for pre- and post-
+ alignment analysis of nanopore sequencing data, quality and error
+ profiles.
+ .
+ NanoOK (pronounced na-nook) is a tool for extraction, alignment and
+ analysis of Nanopore reads. NanoOK will extract reads as FASTA or FASTQ
+ files, align them (with a choice of alignment tools), then generate a
+ comprehensive multi-page PDF report containing yield, accuracy and
+ quality analysis. Along the way, it generates plain text files which can
+ be used for further analysis, as well as graphs suitable for inclusion
+ in presentations and papers.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..582ad47
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: NanoOK
+Upstream-Contact: Richard M. Leggett <richard.leggett at earlham.ac.uk>
+Source: https://github.com/TGAC/NanoOK
+Files-Excluded: *.jar
+
+Files: *
+Copyright: 2015-2017 Richard M. Leggett
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille at debian.org>
+License: GPL-3+
+
+License: GPL-3+
+    This program 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 3 of the License, or
+    (at your option) any later version.
+ .
+    This program 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.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License version 3 or later at /usr/share/common-licenses/GPL-3.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..62983db
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+include /usr/share/dpkg/default.mk
+# this provides:
+# DEB_SOURCE: the source package name
+# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
+# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
+# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
+# DEB_VERSION_UPSTREAM: the package's upstream version
+# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+	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..c4e20f7
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Richard M. Leggett and Darren Heavens and Mario Caccamo and Matthew D. Clark and Robert P. Davey
+  Title: "NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles"
+  Journal: Bioinformatics
+  Year: 2016
+  Volume: 32
+  Number: 1
+  Pages: 142-144
+  DOI: 10.1093/bioinformatics/btv540
+  PMID: 26382197
+  URL: https://academic.oup.com/bioinformatics/article/32/1/142/1743578/NanoOK-multi-reference-alignment-analysis-of
+  eprint: https://academic.oup.com/bioinformatics/article-pdf/32/1/142/16920033/btv540.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..06d513c
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  https://github.com/TGAC/NanoOK/releases .*/archive/v at ANY_VERSION@@ARCHIVE_EXT@

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