Index: debian/control =================================================================== --- debian/control (revision 2565) +++ debian/control (working copy) @@ -1,28 +1,21 @@ -Source: biococoa.app +Source: biococoa Section: science Priority: optional Maintainer: Debian-Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille , Charles Plessy -Build-Depends: debhelper (>= 5), gnustep-make, libgnustep-gui-dev (>= 0.12.0), quilt +Build-Depends: debhelper (>= 5), gnustep-make, libgnustep-gui-dev (>= 0.12.0) Standards-Version: 3.7.3 Homepage: http://bioinformatics.org/biococoa/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biococoa/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/biococoa/trunk/ -Package: biococoa.app +Package: biococoa Architecture: any Depends: ${shlibs:Depends} -Description: biological sequence file format conversion applet for GNUstep - Demo application to demonstrate the possibilities of the BioCocoa framework. +Description: Bioinformatics framework for Cocoa and GNUstep . - This package contains a GNUstep applet to convert between sequence file - formats. The BioCocoa framework provides developers with the opportunity to - add support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE, - Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and TNT - files by writing only three lines of code. The framework is written in Cocoa - (Objective-C). - . - Version 1.6 is the last upstream version that works with GNUstep. If - newer versions are needed to work under Linux try to convince upstream to - support GNUstep. + BioCocoa is an open source framework for bioinformatics + written in Objective-C. It provides Cocoa and GNUstep programmers with + a full suite of APIs for handling and manipulating biological + sequences. Index: debian/dirs =================================================================== --- debian/dirs (revision 2565) +++ debian/dirs (working copy) @@ -1,2 +0,0 @@ -usr/bin -usr/share/lintian/overrides Index: debian/menu =================================================================== --- debian/menu (revision 2565) +++ debian/menu (working copy) @@ -1,2 +0,0 @@ -?package(biococoa.app):needs="X11" section="Applications/Science/Biology"\ - title="BioCocoa" command="/usr/bin/BioCocoa" Index: debian/BioCocoa.desktop =================================================================== --- debian/BioCocoa.desktop (revision 2565) +++ debian/BioCocoa.desktop (working copy) @@ -1,8 +0,0 @@ -[Desktop Entry] -Type=Application -Version=0.94 -Categories=Education;Science;Biology; -Name=BioCocoa -Comment=GNUstep BioCocoa -Icon=/usr/lib/GNUstep/Applications/BioCocoa.app/Resources/biococoa.tiff -Exec=BioCocoa Index: debian/watch =================================================================== --- debian/watch (revision 0) +++ debian/watch (revision 0) @@ -0,0 +1,2 @@ +version=2 +http://www.bioinformatics.org/biococoa/downloads/biococoa-(.+)-src\.tgz Index: debian/patches/04_Interface.patch =================================================================== --- debian/patches/04_Interface.patch (revision 2565) +++ debian/patches/04_Interface.patch (working copy) @@ -1,11 +0,0 @@ ---- biococoa.orig/Interface.m -+++ biococoa/Interface.m -@@ -101,7 +101,7 @@ - backing: NSBackingStoreBuffered - defer: NO]; - -- [self setBackgroundColor:[NSColor colorWithCalibratedRed:0.9254 green:0.91372 blue:0.8470 alpha:1.0]]; -+/* [self setBackgroundColor:[NSColor colorWithCalibratedRed:0.9254 green:0.91372 blue:0.8470 alpha:1.0]]; */ - - [self setInitialFirstResponder: openButton]; - Index: debian/patches/02_Controller.patch =================================================================== --- debian/patches/02_Controller.patch (revision 2565) +++ debian/patches/02_Controller.patch (working copy) @@ -1,13 +0,0 @@ ---- biococoa.orig/Controller.m -+++ biococoa/Controller.m -@@ -49,9 +49,7 @@ - [panel setCanChooseDirectories:NO]; - [panel setPrompt:@"Choose File"]; - [panel runModalForDirectory:nil file:nil types:nil]; -- if ([panel filename]) { -- [self readSequenceFile:[panel filename]]; -- } -+ [self readSequenceFile:[panel filename]]; - } - - Index: debian/patches/05_main.patch =================================================================== --- debian/patches/05_main.patch (revision 2565) +++ debian/patches/05_main.patch (working copy) @@ -1,18 +0,0 @@ ---- biococoa.orig/main.m -+++ biococoa/main.m -@@ -17,7 +17,6 @@ - app = [NSApplication sharedApplication]; - [app setApplicationIconImage: [NSImage imageNamed: @"Calculator.app.tiff"]]; - -- /* - mainMenu = [[NSMenu new]autorelease]; - // Info - [mainMenu addItemWithTitle: @"Info..." -@@ -44,7 +43,6 @@ - keyEquivalent: @"q"]; - - [app setMainMenu: mainMenu]; -- */ - - brain = [Controller new]; - face = [Interface new]; Index: debian/patches/03_GNUmakefile.patch =================================================================== --- debian/patches/03_GNUmakefile.patch (revision 2565) +++ debian/patches/03_GNUmakefile.patch (working copy) @@ -1,27 +0,0 @@ ---- biococoa.orig/GNUmakefile -+++ biococoa/GNUmakefile -@@ -1,12 +1,14 @@ - # GNUmakefile: makefile for Biococoa - # -+# Copyright (C) 1999 Free Software Foundation, Inc. -+# - # Author: Peter Schols - # Date: 2004 - # - # This file is part of GNUstep. - # - # This program is free software; you can redistribute it and/or modify --# it under the terms of the GNU Lesser General Public License as published by -+# it under the terms of the GNU General Public License as published by - # the Free Software Foundation; either version 2 of the License, or - # (at your option) any later version. - # -@@ -25,7 +27,7 @@ - BioCocoa_HEADERS = Controller.h Interface.h BCReader.h BCCreator.h StringAdditions.h - BioCocoa_OBJC_FILES = main.m Controller.m Interface.m BCReader.m BCCreator.m StringAdditions.m - BioCocoa_APPLICATION_ICON = biococoa.tiff --BioCocoa_RESOURCE_FILES = biococoa.tiff -+BioCocoa_RESOURCE_FILES = biococoa.tiff BioCocoaInfo.plist - - include $(GNUSTEP_MAKEFILES)/application.make - Index: debian/patches/01_plist.patch =================================================================== --- debian/patches/01_plist.patch (revision 2565) +++ debian/patches/01_plist.patch (working copy) @@ -1,13 +0,0 @@ ---- biococoa.orig/BioCocoaInfo.plist -+++ biococoa/BioCocoaInfo.plist -@@ -1,7 +1,7 @@ - { -- ApplicationName = BioCocoa -- ApplicationDescription = "GNUstep BioCocoaDemo"; -- ApplicationRelease = BioCocoa 1.6"; -+ ApplicationName = "BioCocoa"; -+ ApplicationDescription = "GNUstep BioCocoa"; -+ ApplicationRelease = "BioCocoa 1.6"; - FullVersionID = "1.6.0 Nov 2004"; - Authors = ("Peter Schols "); - Copyright = "Copyright (C) 2004 The BioCocoa team."; Index: debian/patches/series =================================================================== --- debian/patches/series (revision 2565) +++ debian/patches/series (working copy) @@ -1,5 +0,0 @@ -01_plist.patch -02_Controller.patch -03_GNUmakefile.patch -04_Interface.patch -05_main.patch Index: debian/changelog =================================================================== --- debian/changelog (revision 2565) +++ debian/changelog (working copy) @@ -1,3 +1,10 @@ +biococoa (2.1.0-1) unstable; urgency=low + + * Change package to contain the biococoa libraries instead of + the demo application. + + -- Scott Christley Sun, 05 Oct 2008 13:44:56 -0700 + biococoa.app (1.6.0-8) unstable; urgency=low * Changed the description of the binary package `biococoa.app' to reflect Index: debian/rules =================================================================== --- debian/rules (revision 2565) +++ debian/rules (working copy) @@ -2,19 +2,19 @@ # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 -include /usr/share/quilt/quilt.make +#include /usr/share/quilt/quilt.make include /usr/share/GNUstep/debian/config.mk GNUSTEP_MAKEFILES=$(GS_MAKE_DIR) -build: patch build-stamp +build: build-stamp build-stamp: dh_testdir gs_make touch build-stamp -clean: unpatch +clean: dh_testdir dh_testroot rm -f build-stamp @@ -26,10 +26,10 @@ dh_testroot dh_clean -k dh_installdirs - gs_make install DESTDIR=$(CURDIR)/debian/biococoa.app GNUSTEP_INSTALLATION_DOMAIN=SYSTEM - find `pwd`/debian/biococoa.app -name "*.plist" -exec chmod -x {} \; - dh_install debian/*.desktop usr/share/applications/ - rm $(CURDIR)/debian/*.app/usr/lib/GNUstep/Applications/*.app/Resources/*.desktop + gs_make install DESTDIR=$(CURDIR)/debian/biococoa GNUSTEP_INSTALLATION_DOMAIN=SYSTEM + #find `pwd`/debian/biococoa.app -name "*.plist" -exec chmod -x {} \; + #dh_install debian/*.desktop usr/share/applications/ + #rm $(CURDIR)/debian/*.app/usr/lib/GNUstep/Applications/*.app/Resources/*.desktop # Build architecture-independent files here. binary-indep: build install @@ -40,10 +40,11 @@ dh_testdir dh_testroot dh_installchangelogs - install -m 644 debian/lintian-override $(CURDIR)/debian/biococoa.app/usr/share/lintian/overrides/biococoa.app + #install -m 644 debian/lintian-override $(CURDIR)/debian/biococoa.app/usr/share/lintian/overrides/biococoa.app dh_installdocs dh_installmenu dh_installman + dh_link dh_strip dh_compress dh_fixperms Index: debian/lintian-override =================================================================== --- debian/lintian-override (revision 2565) +++ debian/lintian-override (working copy) @@ -1 +0,0 @@ -biococoa.app: image-file-in-usr-lib