[med-svn] r4875 - in trunk/packages/gentle/trunk/debian: . patches

Sat Jun 5 15:08:03 UTC 2010

Author: moeller
Date: 2010-06-05 15:08:01 +0000 (Sat, 05 Jun 2010)
New Revision: 4875

Added:
   trunk/packages/gentle/trunk/debian/GENtle.1
   trunk/packages/gentle/trunk/debian/patches/remove_clustalw.patch
Removed:
   trunk/packages/gentle/trunk/debian/gentle.1
Modified:
   trunk/packages/gentle/trunk/debian/changelog
   trunk/packages/gentle/trunk/debian/control
   trunk/packages/gentle/trunk/debian/copyright
   trunk/packages/gentle/trunk/debian/docs
   trunk/packages/gentle/trunk/debian/files
   trunk/packages/gentle/trunk/debian/gentle.install
   trunk/packages/gentle/trunk/debian/manpages
   trunk/packages/gentle/trunk/debian/patches/series
   trunk/packages/gentle/trunk/debian/rules
Log:
Further adjustments to remove clustalw,
prepare -dbg package (which does not work)
and lintian cleanliness.


Copied: trunk/packages/gentle/trunk/debian/GENtle.1 (from rev 4857, trunk/packages/gentle/trunk/debian/gentle.1)
===================================================================

--- trunk/packages/gentle/trunk/debian/GENtle.1	                        (rev 0)
+++ trunk/packages/gentle/trunk/debian/GENtle.1	2010-06-05 15:08:01 UTC (rev 4875)
@@ -0,0 +1,22 @@
+.\"                                      Hey, EMACS: -*- nroff -*-
+.TH GENTLE 1 "March  9, 2010"
+.SH NAME
+GENtle \- program to plan genetic cloning experiments
+.SH SYNOPSIS
+.B gentle
+.SH DESCRIPTION
+GENtle integrates a series of programs and databases
+to plan the integration of foreign DNA into another
+larger DNA that by some means can replicate itself
+or is by some other means replicated - a process
+commonly referred to as
+.I cloning.
+.SH OPTIONS
+None.
+.SH SEE ALSO
+.BR http://gentle.magnusmanske.de
+.SH AUTHOR
+GENtle was written by Magnus Manske.
+.PP
+This manual page was written by Steffen Moeller <moeller at debian.org>,
+for the Debian project (and may be used by others).

Modified: trunk/packages/gentle/trunk/debian/changelog
===================================================================
--- trunk/packages/gentle/trunk/debian/changelog	2010-06-05 12:39:30 UTC (rev 4874)
+++ trunk/packages/gentle/trunk/debian/changelog	2010-06-05 15:08:01 UTC (rev 4875)
@@ -1,13 +1,19 @@
-gentle (1.9+cvs20100602+dfsg-1) experimental; urgency=low
+gentle (1.9+cvs20100602+dfsg-1) unstable; urgency=low
 
   * Reupload in reaction to ftp-masters comments (Closes: #582959)
-  * removed tinyurl
+  * removed tinyurl and clustalw from source tree for DFSG compatibility
     - which introduced dependency to quilt
     - and provoked +dfsg suffix to version (not fully correct, yet)
+  * invoking automake, autoconf during build
+    - added those to build-dependencies
+    - removed upstream Makefile and Makefile.in from source
   * declared 1.0 source format
   * removed doc-base lintian warning
   * explicitly listing man page as such
   * added gentle-dbg package
+  * compilation successfullly tested against gcc-4.5
+  * added help/* to package
+  * reupload to unstable
 
  -- Steffen Moeller <moeller at debian.org>  Wed, 02 Jun 2010 12:07:21 +0200
 

Modified: trunk/packages/gentle/trunk/debian/control
===================================================================
--- trunk/packages/gentle/trunk/debian/control	2010-06-05 12:39:30 UTC (rev 4874)
+++ trunk/packages/gentle/trunk/debian/control	2010-06-05 15:08:01 UTC (rev 4875)
@@ -1,8 +1,8 @@
 Source: gentle
-Section: non-free/science
+Section: science
 Priority: optional
 Maintainer: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper (>= 7), autotools-dev, libwxgtk2.8-dev, quilt, cdbs, libtinyxml-dev
+Build-Depends: debhelper (>= 7), autotools-dev, libwxgtk2.8-dev, quilt, cdbs, libtinyxml-dev, automake, autoconf
 Standards-Version: 3.8.4
 Homepage: http://gentle.magnusmanske.de
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gentle/trunk/?rev=0&sc=0
@@ -11,6 +11,7 @@
 Package: gentle
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: clustalw
 Description: suite to plan genetic cloning
  GENtle is a software for DNA and amino acid editing, database management,
  plasmid maps, restriction and ligation, alignments, sequencer data
@@ -19,10 +20,15 @@
 Package: gentle-dbg
 Architecture: any
 Depends: gentle, ${shlibs:Depends}, ${misc:Depends}
+Section: debug
+Priority: extra
 Recommends: libtinyxml2.5.3-dbg
 Description: debug symbols for gentle suite for genetic cloning
  As every suite working with a series of independently developed
  programs, also GENtle tends to be perceived as rather complex.
  This package prepares users and developers to communicate
  over hunting and eliminating bugs.
+ .
+ Well, this package is not functional for the time speaking.
+ Help would be appreciated.
  

Modified: trunk/packages/gentle/trunk/debian/copyright
===================================================================
--- trunk/packages/gentle/trunk/debian/copyright	2010-06-05 12:39:30 UTC (rev 4874)
+++ trunk/packages/gentle/trunk/debian/copyright	2010-06-05 15:08:01 UTC (rev 4875)
@@ -6,45 +6,15 @@
 
     http://gentle.magnusmanske.de/
 
-Files: clustalw/*
+Files: ipc/*
+Author: Dirk Nolting <nolting at uni-duesseldorf.de>
+Copyright: (C) 2001 Dirk Nolting <nolting at uni-duesseldorf.de>
+License: GPL-2+
 
-Upstream Authors:
-    Toby J. Gibson <gibson at embl-heidelberg.de>
-    J. D. Thompson <thompson at igbmc.u-strasbg.fr>
-    Des G. Higgins <d.higgins at ucc.ie>
+Files: wav/*
+Copyright: Voxeo Corporation (http://evolution.voxeo.com)
+License: LGPL
 
-Copyright:
-    The authors and their respective employers.
-
-License:
-
-    ******************************************************************************
-    
-                   CLUSTAL W Multiple Sequence Alignment Program
-                            (version 1.83, Feb 2003)
-    
-    ******************************************************************************
-
-
-    Please send bug reports, comments etc. to one of:-
-	gibson at embl-heidelberg.de
-	thompson at igbmc.u-strasbg.fr
-	d.higgins at ucc.ie
-
-
-    ******************************************************************************
-
-                      POLICY ON COMMERCIAL DISTRIBUTION OF CLUSTAL W
-
-    Clustal W is freely available to the user community. However, Clustal W is
-    increasingly being distributed as part of commercial sequence analysis
-    packages. To help us safeguard future maintenance and development, commercial
-    distributors of Clustal W must take out a NON-EXCLUSIVE LICENCE. Anyone
-    wishing to commercially distribute version 1.81 of Clustal W should contact the
-    authors unless they have previously taken out a licence.
-    
-    ******************************************************************************
-
 Files: *
 
 Upstream Author:

Modified: trunk/packages/gentle/trunk/debian/docs
===================================================================
--- trunk/packages/gentle/trunk/debian/docs	2010-06-05 12:39:30 UTC (rev 4874)
+++ trunk/packages/gentle/trunk/debian/docs	2010-06-05 15:08:01 UTC (rev 4875)
@@ -1,5 +1,4 @@
 docs/GENtle*en*.pdf
 NEWS
-README.Ubuntu
 RELEASE-NOTES.txt
 tips_en.txt

Modified: trunk/packages/gentle/trunk/debian/files
===================================================================
--- trunk/packages/gentle/trunk/debian/files	2010-06-05 12:39:30 UTC (rev 4874)
+++ trunk/packages/gentle/trunk/debian/files	2010-06-05 15:08:01 UTC (rev 4875)
@@ -1 +1,4 @@
-gentle_1.9+cvs20100308-1_amd64.deb non-free/science optional
+gentle_1.9+cvs20100602+dfsg-1_amd64.deb science optional
+gentle-dbg_1.9+cvs20100602+dfsg-1_amd64.deb debug extra
+gentle_1.9+cvs20100602+dfsg-1_amd64.deb science optional
+gentle-dbg_1.9+cvs20100602+dfsg-1_amd64.deb debug extra

Deleted: trunk/packages/gentle/trunk/debian/gentle.1
===================================================================
--- trunk/packages/gentle/trunk/debian/gentle.1	2010-06-05 12:39:30 UTC (rev 4874)
+++ trunk/packages/gentle/trunk/debian/gentle.1	2010-06-05 15:08:01 UTC (rev 4875)
@@ -1,22 +0,0 @@
-.\"                                      Hey, EMACS: -*- nroff -*-
-.TH GENTLE 1 "March  9, 2010"
-.SH NAME
-gentle \- program to plan genetic cloning experiments
-.SH SYNOPSIS
-.B gentle
-.SH DESCRIPTION
-GENtle integrates a series of programs and databases
-to plan the integration of foreign DNA into another
-larger DNA that by some means can replicate itself
-or is by some other means replicated - a process
-commonly referred to as
-.I cloning.
-.SH OPTIONS
-None.
-.SH SEE ALSO
-.BR http://gentle.magnusmanske.de
-.SH AUTHOR
-GENtle was written by Magnus Manske.
-.PP
-This manual page was written by Steffen Moeller <moeller at debian.org>,
-for the Debian project (and may be used by others).

Modified: trunk/packages/gentle/trunk/debian/gentle.install
===================================================================
--- trunk/packages/gentle/trunk/debian/gentle.install	2010-06-05 12:39:30 UTC (rev 4874)
+++ trunk/packages/gentle/trunk/debian/gentle.install	2010-06-05 15:08:01 UTC (rev 4875)
@@ -1,4 +1,5 @@
 wav	/usr/share/gentle/
+help	/usr/share/gentle/
 variables.csv	/usr/share/gentle/
 bitmaps	/usr/share/gentle/
 codon_catalog.csv	/usr/share/gentle/

Modified: trunk/packages/gentle/trunk/debian/manpages
===================================================================
--- trunk/packages/gentle/trunk/debian/manpages	2010-06-05 12:39:30 UTC (rev 4874)
+++ trunk/packages/gentle/trunk/debian/manpages	2010-06-05 15:08:01 UTC (rev 4875)
@@ -1 +1 @@
-debian/gentle.1
+debian/GENtle.1

Added: trunk/packages/gentle/trunk/debian/patches/remove_clustalw.patch
===================================================================
--- trunk/packages/gentle/trunk/debian/patches/remove_clustalw.patch	                        (rev 0)
+++ trunk/packages/gentle/trunk/debian/patches/remove_clustalw.patch	2010-06-05 15:08:01 UTC (rev 4875)
@@ -0,0 +1,42 @@
+Index: gentle-1.9+20100602+dfsg/Makefile.am
+===================================================================
+--- gentle-1.9+20100602+dfsg.orig/Makefile.am	2010-06-05 16:36:41.000000000 +0200
++++ gentle-1.9+20100602+dfsg/Makefile.am	2010-06-05 16:36:41.000000000 +0200
+@@ -137,24 +137,6 @@
+ TPhyloTree.cpp\
+ PCR_Troubleshoot.cpp\
+ TProteolysis.cpp\
+-clustalw/alnscore.cpp\
+-clustalw/amenu.cpp\
+-clustalw/calcgap.cpp\
+-clustalw/calcprf1.cpp\
+-clustalw/calcprf2.cpp\
+-clustalw/calctree.cpp\
+-clustalw/clustalw.cpp\
+-clustalw/gcgcheck.cpp\
+-clustalw/interfac.cpp\
+-clustalw/malign.cpp\
+-clustalw/palign.cpp\
+-clustalw/prfalign.cpp\
+-clustalw/random.cpp\
+-clustalw/readmat.cpp\
+-clustalw/sequence.cpp\
+-clustalw/showpair.cpp\
+-clustalw/trees.cpp\
+-clustalw/util.cpp\
+ ipc/element.cpp\
+ ipc/gp_out.cpp\
+ ipc/ipc.cpp\
+@@ -231,12 +213,6 @@
+ TPhyloTree.h\
+ TEliteLaChromLogDialog.h\
+ ncoils.h\
+-clustalw/clustalw.h\
+-clustalw/dayhoff.h \
+-clustalw/general.h \
+-clustalw/matrices.h \
+-clustalw/param.h \
+-clustalw/xmenu.h\
+ ipc/element.h\
+ ipc/global.h\
+ ipc/gp_out.h\

Modified: trunk/packages/gentle/trunk/debian/patches/series
===================================================================
--- trunk/packages/gentle/trunk/debian/patches/series	2010-06-05 12:39:30 UTC (rev 4874)
+++ trunk/packages/gentle/trunk/debian/patches/series	2010-06-05 15:08:01 UTC (rev 4875)
@@ -1 +1,2 @@
 remove_tinyxml.patch
+remove_clustalw.patch

Modified: trunk/packages/gentle/trunk/debian/rules
===================================================================
--- trunk/packages/gentle/trunk/debian/rules	2010-06-05 12:39:30 UTC (rev 4874)
+++ trunk/packages/gentle/trunk/debian/rules	2010-06-05 15:08:01 UTC (rev 4875)
@@ -11,9 +11,9 @@
 
 include /usr/share/cdbs/1/rules/patchsys-quilt.mk
 
-CXXFLAGS="-D__DEBIAN__ -O2 -g -Wno-write-strings"
+CXXFLAGS="-D__DEBIAN__ -O2 -g -Wno-write-strings -DUSE_EXTERNAL_CLUSTALW"
 
-configure: patch configure-stamp
+configure: configure-stamp
 configure-stamp:
 	dh_testdir
 	echo "configuring with own configure!"
@@ -24,7 +24,7 @@
 	touch $@
 
 build build-arch:	build-stamp
-build-stamp: configure-stamp
+build-stamp: patch configure-stamp
 	dh_testdir
 	echo "building with own build!"
 	$(MAKE) CXXFLAGS=$(CXXFLAGS) 
@@ -52,6 +52,9 @@
 	dh_builddeb
 
 install install-arch: build-stamp
+	dh_install
+	find debian -name "*.png" -o -name "*.htm" -o -name "*.xpm" -o -name "*.bmp" -o "*.txt" -o "*.csv" | xargs -r chmod -x
+	find debian -name "license.txt" | xargs -r rm
 
 install-indep:
 	echo Nothing to do for install-indep
@@ -60,7 +63,7 @@
 	#$(MAKE) -f debian/rules DH_OPTIONS=-i binary-common
 	echo Nothing to do for binary-indep
 
-binary-arch: build-arch
+binary-arch: install-arch
 	$(MAKE) -f debian/rules DH_OPTIONS=-s binary-common
 
 binary: binary-arch binary-indep
@@ -69,7 +72,7 @@
 	dh_testdir
 	dh_testroot
 	find . -name "*.o"  | xargs -r rm
-	dh_clean build-arch-stamp build-indep-stamp configure-stamp
+	dh_clean build-arch-stamp build-indep-stamp configure-stamp build-stamp
 
 
 
@@ -87,5 +90,6 @@
 	cvs -z3 -d:pserver:anonymous at gentle-m.cvs.sourceforge.net:/cvsroot/gentle-m co -P GENtle
 	mv GENtle "gentle-$(VERSION)"
 	GZIP=-9 tar --exclude Makefile.in --exclude Makefile --exclude CVS --exclude tinyxml \
-		    --exclude .deps --exclude .cvsignore \
+		    --exclude .deps --exclude .cvsignore --exclude Makefile.in --exclude Makefile.linux \
+		    --exclude clustalw \
 		    -czvf "gentle_$(VERSION).orig.tar.gz" "gentle-$(VERSION)"


