[med-svn] [plato] 07/12: Normalise packaging, add citation
Andreas Tille
tille at debian.org
Mon Dec 18 19:43:40 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository plato.
commit fcc1277be92399ac1f737ffc85042f8eeb6853b9
Author: Andreas Tille <tille at debian.org>
Date: Tue Jan 3 16:19:04 2017 +0000
Normalise packaging, add citation
---
debian/README.Debian | 6 ------
debian/README.source | 9 ---------
debian/compat | 2 +-
debian/control | 23 ++++++++++++-----------
debian/copyright | 15 +++++----------
debian/rules | 14 +-------------
debian/upstream/metadata | 10 ++++++++++
debian/watch | 8 ++++++--
8 files changed, 35 insertions(+), 52 deletions(-)
diff --git a/debian/README.Debian b/debian/README.Debian
deleted file mode 100644
index ae35857..0000000
--- a/debian/README.Debian
+++ /dev/null
@@ -1,6 +0,0 @@
-plato for Debian
-----------------
-
-<possible notes regarding this package - if none, delete this file>
-
- -- Steffen Moeller <moeller at debian.org> Wed, 14 Sep 2011 14:47:35 +0200
diff --git a/debian/README.source b/debian/README.source
deleted file mode 100644
index 6ab95e2..0000000
--- a/debian/README.source
+++ /dev/null
@@ -1,9 +0,0 @@
-plato for Debian
-----------------
-
-<this file describes information about the source package, see Debian policy
-manual section 4.14. You WILL either need to modify or delete this file>
-
-
-
-
diff --git a/debian/compat b/debian/compat
index 45a4fb7..f599e28 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-8
+10
diff --git a/debian/control b/debian/control
index 6250ddf..ef45c28 100644
--- a/debian/control
+++ b/debian/control
@@ -1,19 +1,19 @@
Source: plato
-Section: science
-Priority: extra
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper (>= 8.0.0),
- libboost-dev
-Standards-Version: 3.9.2
-Homepage: https://chgr.mc.vanderbilt.edu/plato
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/plato/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/plato/trunk
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 10),
+ libboost-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/plato/trunk
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/plato/trunk/
+Homepage: https://ritchielab.psu.edu/plato
Package: plato
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
Description: Analysis, translation, and organization of large-scale genetic data
PLATO is an acronym for "PLatform for the Analysis, Translation,
and Organization of large-scale data". Recent technological advances
@@ -55,7 +55,8 @@ Description: Analysis, translation, and organization of large-scale genetic data
Package: plato-dbg
Architecture: any
-Depends: ${misc:Depends}, plato (= ${binary:Version})
+Depends: ${misc:Depends},
+ plato (= ${binary:Version})
Description: debug information for plato
plato is dominate by a single binary. This package adds debug
symbols to it.
diff --git a/debian/copyright b/debian/copyright
index b3d199c..a2827a6 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,15 +1,16 @@
-Format: http://dep.debian.net/deps/dep5
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: plato
-Source: <url://example.com>
+Source: https://ritchielab.psu.edu/plato
Files: *
-Copyright: <years> <put author's name and email here>
- <years> <likewise for another author>
+Copyright: 2008-2016 Marylyn Ritchie and others
License: GPL-2+
Files: debian/*
Copyright: 2011 Steffen Moeller <moeller at debian.org>
License: GPL-2+
+
+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
@@ -20,11 +21,5 @@ License: GPL-2+
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".
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
diff --git a/debian/rules b/debian/rules
index 7e2980a..fcfc3e8 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,5 +1,4 @@
#!/usr/bin/make -f
-# -*- makefile -*-
# Uncomment this to turn on verbose mode.
export DH_VERBOSE=1
@@ -7,19 +6,8 @@ export DH_VERBOSE=1
%:
dh $@
-
override_dh_auto_test:
# do not test, missing cdblib.h
-override_dh_strip:
- dh_strip --dbg-package plato-dbg
-
-VERSION=1.1
get-orig-source:
- [ -r ../plato-$(VERSION).tar.gz ] || wget -O ../plato-$(VERSION).tar.gz http://chgr.mc.vanderbilt.edu/ritchielab/software/builds/plato/plato-release$(VERSION).tar.gz
- cd .. && tar xzf plato-$(VERSION).tar.gz
- cd .. && mv plato-release plato-$(VERSION)
- cd ../plato-$(VERSION) && make clean
- find ../plato-$(VERSION) -name "*.cpp" -o -name "*.h" | xargs -r chmod -x
- find ../plato-$(VERSION) -name "*.svn" -a -type d | xargs -r rm -rf
- cd .. && tar cjf plato_$(VERSION).orig.tar.bz2 plato-$(VERSION)
+ echo "Download latest version from https://ritchielab.psu.edu/plato"
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..68638b5
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,10 @@
+Reference:
+ Author: "Benjamin J. Grady and Eric Torstenson and Scott M. Dudek and Justin Giles and David Sexton and Marylyn D. Ritchie"
+ Title: "Finding unique filter sets in PLATO: a precursor to efficient interaction analysis in GWAS data"
+ Journal: Proceedings of the Pacific Symposium
+ Year: 2010
+ Pages: 315-26
+ DOI: 10.1142/9789814295291_0034
+ PMID: 19908384
+ URL: http://www.worldscientific.com/doi/abs/10.1142/9789814295291_0034
+ eprint: http://www.worldscientific.com/doi/pdf/10.1142/9789814295291_0034
diff --git a/debian/watch b/debian/watch
index f7da17a..155c0ab 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,2 +1,6 @@
-version=3
-http://chgr.mc.vanderbilt.edu/ritchielab/software/builds/plato/plato-release([0-9.]+)\.tar\.gz
+# FIXME: Session handling prevents download of the real tar archive.
+# May be debian-mentors at lists.debian.org could be of any help
+
+version=4
+
+https://ritchielab.psu.edu/plato .*session.php.*file=plato-(\d[.\d]+)\.tar\.gz
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