[med-svn] [placnet] 02/03: Add initial packaging

Andreas Tille tille at debian.org
Mon Oct 12 13:12:43 UTC 2015 

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

tille pushed a commit to branch master
in repository placnet.

commit 0ac39aeeba5a660f8b17cd2f4339d520adbc9c05
Author: Andreas Tille <tille at debian.org>
Date:   Mon Oct 12 15:07:44 2015 +0200

    Add initial packaging
---
 debian/changelog         |   5 +
 debian/compat            |   1 +
 debian/control           |  24 ++++
 debian/copyright         | 290 +++++++++++++++++++++++++++++++++++++++++++++++
 debian/get-orig-source   |  34 ++++++
 debian/rules             |  15 +++
 debian/source/format     |   1 +
 debian/upstream/metadata |  12 ++
 debian/watch             |   1 +
 9 files changed, 383 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..2dd386f
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+placnet (1.03-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Mon, 12 Oct 2015 14:42:07 +0200
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..c974f65
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: placnet
+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: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/placnet.git
+Vcs-Git: git://anonscm.debian.org/debian-med/placnet.git
+Homepage: http://sourceforge.net/projects/placnet/
+
+Package: placnet
+Architecture: all
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: Plasmid Constellation Network project
+ Placnet is a new tool for plasmid analysis in NGS projects. Placnet has
+ been written in Perl. It's been optimized to work with Illumina
+ sequences but it also works with 454, Iontorrent or any of the actual
+ sequence technologies.
+ .
+ The input of placnet is a set of contigs and one or more SAM files with
+ the mapping of the reads against the contigs. Placnet obtains a set of
+ files, easily opened on Cytoscape software or other network tools.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..f8b29f7
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,290 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Placnet
+Source: http://sourceforge.net/projects/placnet/files/
+
+Files: *
+Copyright: 2013-2015 María de Toro
+License: CC-BY
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: CC-BY
+
+License: CC-BY
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diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..9b41f9f
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,34 @@
+#!/bin/sh
+# if you need to repack for whatever reason you can
+# use this script via uscan or directly
+#
+# FIXME: currently the code is not conform to Debian Policy
+#        http://www.debian.org/doc/debian-policy/ch-source.html
+#        "get-orig-source (optional)"
+#        This target may be invoked in any directory, ...
+# --> currently it is assumed the script is called in the
+#     source directory featuring the debian/ dir
+
+COMPRESS=xz
+
+set -e
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+
+TARDIR=${NAME}-${VERSION}
+
+mkdir -p ../tarballs
+cd ../tarballs
+mkdir -p ${TARDIR}
+cd ${TARDIR}
+wget -q http://heanet.dl.sourceforge.net/project/placnet/placnet.pl
+DOWNLOADVERSION=`grep '^#v[0-9]' placnet.pl | sed 's/^#v//'`
+if [ "${VERSION}" != "${DOWNLOADVERSION}" ] ; then
+    echo "The downloaded version $DOWNLOADVERSION does not fit the Debian version $VERSION."
+    echo "Please adapt debian/changelog."
+    exit 1
+fi
+cd ..
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..9361f48
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,15 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+%:
+	dh $@
+
+override_dh_install:
+	mkdir -p debian/$(DEBPKGNAME)/usr/bin
+	cp -a placnet.pl debian/$(DEBPKGNAME)/usr/bin/placnet
+
+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..769b758
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Val F. Lanza and María de Toro and M. Pilar Garcillán-Barcia and Azucena Mora and Jorge Blanco and Teresa M. Coque and Fernando de la Cruz
+  Title: "Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences"
+  Journal: PLOS
+  Year: 2014
+  Volume: 10
+  Number: 12
+  Pages: e1004766
+  DOI: 10.1371/journal.pgen.1004766
+  PMID: 25522143
+  URL: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004766
+  eprint: http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004766&representation=PDF
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..d8ef91e
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1 @@
+# There is no tarball download location, this software is only available in SVN

-- 
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