[med-svn] [beads] 02/02: Initial Debian packaging
Andreas Tille
tille at debian.org
Thu Oct 19 14:06:44 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository beads.
commit 85cb7c5ca8974ac0a1297769ec87c8c1969c8ace
Author: Andreas Tille <tille at debian.org>
Date: Thu Oct 19 16:06:17 2017 +0200
Initial Debian packaging
---
debian/changelog | 154 +----------------------------------------------
debian/compat | 2 +-
debian/control | 23 ++++---
debian/copyright | 16 +++--
debian/patches/qt5.patch | 33 ++++++++++
debian/patches/series | 1 +
debian/rules | 89 ++-------------------------
debian/source/format | 1 +
debian/upstream/metadata | 11 ++++
debian/watch | 3 +
10 files changed, 83 insertions(+), 250 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 8779d55..a45fc32 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,153 +1,5 @@
-beads (1.1.13-1~lucid1) lucid; urgency=low
+beads (1.1.13-1) UNRELEASED; urgency=medium
- * fixed bug when trying to save results from sypro images (detected by T. Balliau)
+ * Initial upload to Debian (Closes: #???)
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 9 Sep 2010 10:18:51 +0200
-
-beads (1.1.12-1~lucid1) lucid; urgency=low
-
- * command line output extension detection problem fixed
- * integration of Cimg 1.3.9
- * memory leak fixed on qt properties object
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 26 Aug 2010 10:18:51 +0200
-
-beads (1.1.11-1~lucid1) lucid; urgency=low
-
- * UTF8 image file path
- * parameter "atom" renamed in "minbeads"
- * rename CONFLUENTS image to SELECT image
- * parameter "minconfl" renamed in "minpath"
- * parameter "flux" renamed in "minflux"
- * confluent_ prefix removed from minflux, minpath, winconfl, minbeads
- * prob_ prefix removed from sx, sy, sx_bottom, sy_bottom
- * rename detection_threshold to minproba
- * rename quantification_npass to npass
- * inverse image checked by default
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 18 May 2010 10:18:51 +0200
-
-beads (1.1.10-1~lucid1) lucid; urgency=low
-
- * write matchset with matched spot num
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Mon, 10 Apr 2010 10:18:51 +0200
-
-beads (1.1.9-2~lucid1) lucid; urgency=low
-
- * bug fixed writing sample name in PROTICdbML (thanks to Thierry Balliau)
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 28 Apr 2010 10:18:51 +0200
-
-beads (1.1.9-1~lucid1) karmic; urgency=low
-
- * edit spot_num dialog
- * new menu item to save all beads steps in one directory (PROBABILITIES, NUMBERS, PATH...)
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 28 Apr 2010 10:18:51 +0200
-
-beads (1.1.8-1~karmic1) karmic; urgency=low
-
- * poor protection of detection in BeadsResults fixed (bug found by Thierry Balliau)
- * gnumeric support
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Fri, 12 Mar 2010 10:18:51 +0200
-
-beads (1.1.7-1~karmic1) karmic; urgency=low
-
- * CMakeLists.txt changes
- * use of QXmlStreamWriter to produce well formed and well coded XML documents
- * use of QString and QDebug in the core library
- * qt about disabled
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Fri, 24 Feb 2010 10:18:51 +0200
-
-beads (1.1.6-1~karmic1) karmic; urgency=low
-
- * bug reported by Thierry Balliau fixed (depth of recursive functions)
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 13 Jan 2010 02:18:51 +0200
-
-beads (1.1.5-1~karmic1) karmic; urgency=low
-
- * cimg_OS defined by cmake
- * SVG beads icon added to the main windows
- * image intensity reads correctly UTF8 file paths (uses QFileInfo)
- * action "fit to windows" is disabled
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 16 Dec 2009 02:18:51 +0200
-
-beads (1.1.4-1~karmic1) karmic; urgency=low
-
- * save picked num in PROTICdbML file
- * edit picked num on detected gel image
- * display spot number on detected gel image
- * display x,y position of the cursor on gel image
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 16 Dec 2009 02:18:51 +0200
-
-beads (1.1.3-1~karmic1) karmic; urgency=low
-
- * contour edges problem fixed
- * qt compilation with win32
- * new steps argument
- * updated man page
- * desktop menu for qtbeads
- * parameters files examples in /usr/share/beads
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Mon, 7 Dec 2009 18:18:51 +0200
-
-beads (1.1.2-1~karmic1) karmic; urgency=low
-
- * load beads parameter file
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 30 Nov 2009 10:18:51 +0200
-
-beads (1.1.1-2~karmic1) karmic; urgency=low
-
- * package dependencies fixed
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 29 Nov 2009 10:18:51 +0200
-
-beads (1.1.1-1~karmic1) karmic; urgency=low
-
- * saves results to output files (images, quantifications, svg, PROTICdbML)
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 29 Nov 2009 10:18:51 +0200
-
-beads (1.1.0-1~karmic1) karmic; urgency=low
-
- * new cimg library (1.3.2)
- * first version of qtbeads, GUI for beads
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 28 Nov 2009 10:18:51 +0200
-
-beads (1.0-2~karmic1) karmic; urgency=low
-
- * repackaging for Ubuntu Karmic Koala
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 12 Nov 2009 10:18:51 +0200
-
-beads (1.0-1~hardy1) hardy; urgency=low
-
- * published in Proteomics : http://www.ncbi.nlm.nih.gov/pubmed/19003871
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 26 Nov 2008 11:18:51 +0200
-
-beads (1.0-1) intrepid; urgency=low
-
- * published in Proteomics : http://www.ncbi.nlm.nih.gov/pubmed/19003871
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 26 Nov 2008 11:18:51 +0200
-
-beads (0.1-1~hardy1) hardy; urgency=low
-
- * ppa build for Hardy and Intrepid.
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Fri, 07 Nov 2008 20:08:38 +0200
-
-beads (0.1-1) intrepid; urgency=low
-
- * Initial release.
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 25 Jun 2008 11:18:51 +0200
+ -- Andreas Tille <tille at debian.org> Thu, 19 Oct 2017 14:58:04 +0200
diff --git a/debian/compat b/debian/compat
index b8626c4..f599e28 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-4
+10
diff --git a/debian/control b/debian/control
index b381868..c5915ea 100644
--- a/debian/control
+++ b/debian/control
@@ -1,15 +1,22 @@
Source: beads
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Langella <olivier.langella at moulon.inra.fr>
Section: science
Priority: optional
-Maintainer: Olivier Langella <olivier.langella at moulon.inra.fr>
-Homepage: http://pappso.inra.fr/bioinfo/beads
-DM-Upload-Allowed: yes
-Uploaders: Olivier Langella <olivier.langella at moulon.inra.fr>
-Standards-Version: 1.0
-Build-Depends: debhelper (>= 5), cmake (>= 2), libx11-dev, libc6-dev,libqt4-dev (>= 4.5.2)
+Build-Depends: debhelper (>= 10),
+ cmake,
+ qtbase5-dev
+Standards-Version: 4.1.1
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/beads.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/beads.git
+Homepage: http://moulon.inra.fr/beads/beads.html
Package: beads
Architecture: any
-Depends: ${shlibs:Depends}, libx11-6, imagemagick,libqtgui4 (>= 4.5.2),libqt4-xml (>= 4.5.2),libqt4-svg (>= 4.5.2)
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ imagemagick
Description: 2-DE electrophoresis gel image spot detection
- 2-DE electrophoresis gel image spot detection
\ No newline at end of file
+ BEADS is a program for spot detection on 2-D gel images. It is based on
+ an analogy with beads flowing uphill on the surface of the gel image and
+ on the analysis of their paths (Langella & Zivy, 2008).
diff --git a/debian/copyright b/debian/copyright
index 8051220..23e54c1 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,9 +1,13 @@
-X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Olivier Langella <olivier.langella at moulon.inra.fr>
-X-Debianized-Date: Wed, 25 Jun 2008 11:18:51 +0200
-X-Source-Downloaded-From:
-X-Upstream-Author:
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BEADS
+Upstream-Contact: Olivier Langella <olivier.langella at moulon.inra.fr>
+Source: http://pappso.inra.fr/bioinfo/beads/index.php
Files: *
-Copyright: © 2008 Michel Zivy <zivy at moulon.inra.fr>, Olivier Langella <olivier.langella at moulon.inra.fr>
+Copyright: 2008-2010 Michel Zivy <zivy at moulon.inra.fr>, Olivier Langella <olivier.langella at moulon.inra.fr>
License: CeCILL
+
+Files: debian/*
+Copyright: Andreas Tille <tille at debian.org>
+License: CeCILL
+
diff --git a/debian/patches/qt5.patch b/debian/patches/qt5.patch
new file mode 100644
index 0000000..9024e1a
--- /dev/null
+++ b/debian/patches/qt5.patch
@@ -0,0 +1,33 @@
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -1,7 +1,7 @@
+
+- # this command finds Qt4 libraries and sets all required variables
+- # note that it's Qt4, not QT4 or qt4
+-FIND_PACKAGE( Qt4 REQUIRED )
++ # this command finds Qt5 libraries and sets all required variables
++ # note that it's Qt5, not QT5 or qt5
++FIND_PACKAGE( Qt5 REQUIRED )
+
+
+ # add some useful macros and variables
+@@ -65,4 +65,4 @@ ELSE(WIN32)
+ target_link_libraries (beads ${X11_LIBRARIES} m ${PTHREADS_LIBRARY} ${EXTRA_CIMG_LIBRARY} ${QT_LIBRARIES} )
+ ENDIF(WIN32)
+
+-SUBDIRS (qtbeads)
+\ No newline at end of file
++SUBDIRS (qtbeads)
+--- a/src/qtbeads/CMakeLists.txt
++++ b/src/qtbeads/CMakeLists.txt
+@@ -1,7 +1,7 @@
+
+- # this command finds Qt4 libraries and sets all required variables
+- # note that it's Qt4, not QT4 or qt4
+-FIND_PACKAGE( Qt4 REQUIRED )
++ # this command finds Qt5 libraries and sets all required variables
++ # note that it's Qt5, not QT5 or qt5
++FIND_PACKAGE( Qt5 REQUIRED )
+
+
+ # add some useful macros and variables
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..912bc1f
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+qt5.patch
diff --git a/debian/rules b/debian/rules
index aa141b1..07a9687 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,91 +1,12 @@
#!/usr/bin/make -f
-# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
+CMAKE_EXTRA_FLAGS += -DQ_OS_X11=ON
+%:
+ dh $@
-
-configure: configure-stamp
-configure-stamp:
- cmake -DCMAKE_INSTALL_PREFIX=/usr .
- dh_testdir
- # Add here commands to configure the package.
-
- touch configure-stamp
-
-
-build: build-stamp
-
-build-stamp: configure-stamp
- dh_testdir
-
- # Add here commands to compile the package.
- $(MAKE)
- #docbook-to-man debian/beads.sgml > beads.1
-
- touch $@
-
-clean:
- dh_testdir
- dh_testroot
- rm -f build-stamp configure-stamp CMakeCache.txt
-
- # Add here commands to clean up after the build process.
- -$(MAKE) clean
-
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs
-
- # Add here commands to install the package into debian/beads.
- $(MAKE) DESTDIR=$(CURDIR)/debian/beads install
-
-
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
-
-# Build architecture-dependent files here.
-binary-arch: build install
- dh_testdir
- dh_testroot
-# dh_installchangelogs ChangeLog
- dh_installdocs
- dh_installexamples
-# dh_install
-# dh_installmenu
-# dh_installdebconf
-# dh_installlogrotate
-# dh_installemacsen
-# dh_installpam
-# dh_installmime
-# dh_python
-# dh_installinit
-# dh_installcron
-# dh_installinfo
- dh_installman
- dh_link
- dh_strip
- dh_compress
- dh_fixperms
-# dh_perl
-# dh_makeshlibs
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
+override_dh_auto_configure:
+ dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
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..07b8d32
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Olivier Langella and Michel Zivy
+ Title: "A method based on bead flows for spot detection on 2-D gel images"
+ Journal: Proteomics
+ Year: 2008
+ Volume: 8
+ Number: 23-24
+ Pages: 4914-8
+ DOI: 10.1002/pmic.200800644
+ PMID: 19003871
+ URL: http://onlinelibrary.wiley.com/doi/10.1002/pmic.200800644/abstract
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..46f0b39
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+http://pappso.inra.fr/bioinfo/beads/index.php .*/downloads/beads- at ANY_VERSION@@ARCHIVE_EXT@
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