--- garlic-1.6.orig/debian/rules +++ garlic-1.6/debian/rules @@ -0,0 +1,20 @@ +#!/usr/bin/make -f + +include /usr/share/cdbs/1/rules/buildcore.mk +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/class/langcore.mk + +PACKAGE := garlic + +build: build-arch +build-arch: + $(MAKE) CCOPT="$(CFLAGS)" + cp .garlicrc garlicrc + +clean:: + rm -f *.o garlic + rm -f garlicrc + +binary/garlic:: + chmod 644 *.script + --- garlic-1.6.orig/debian/install +++ garlic-1.6/debian/install @@ -0,0 +1,4 @@ +garlic usr/bin/ +garlicrc etc/ +debian/garlic.desktop usr/share/applications/ +garlic.xpm usr/share/pixmaps/ --- garlic-1.6.orig/debian/control +++ garlic-1.6/debian/control @@ -0,0 +1,40 @@ +Source: garlic +Section: science +Priority: optional +Maintainer: Debichem Team +Uploaders: Michael Banck +Build-Depends: debhelper (>> 5), cdbs, libx11-dev +Standards-Version: 3.7.3 +Homepage: http://www.zucic.org/garlic/ +Vcs-Browser: http://svn.debian.org/wsvn/debichem/ +Vcs-Svn: svn+ssh://svn.debian.org/svn/debichem/unstable/garlic/ +XS-DM-Upload-Allowed: yes + +Package: garlic +Architecture: any +Depends: ${shlibs:Depends} +Suggests: garlic-doc, openbabel +Description: A visualization program for biomolecules + Garlic is written for the investigation of membrane proteins. It may be + used to visualize other proteins, as well as some geometric objects. + This version of garlic recognizes PDB format version 2.1. Garlic may + also be used to analyze protein sequences. + . + It only depends on the X libraries, no other libraries are needed. + . + Features include: + - The slab position and thickness are visible in a small window. + - Atomic bonds as well as atoms are treated as independent drawable + objects. + - The atomic and bond colors depend on position. Five mapping modes + are available (as for slab). + - Capable to display stereo image. + - Capable to display other geometric objects, like membrane. + - Atomic information is available for atom covered by the mouse + pointer. No click required, just move the mouse pointer over the + structure! + - Capable to load more than one structure. + - Capable to draw Ramachandran plot, helical wheel, Venn diagram, + averaged hydrophobicity and hydrophobic moment plot. + - The command prompt is available at the bottom of the main window. + It is able to display one error message and one command string. --- garlic-1.6.orig/debian/changelog +++ garlic-1.6/debian/changelog @@ -0,0 +1,156 @@ +garlic (1.6-1.1) unstable; urgency=low + + * Non-maintainer upload. + * Fix "FTBFS: cp: cannot stat `./garlic': No such file or directory": + add build-arch target in debian/rules. + (Closes: #666285) + + -- gregor herrmann Sun, 15 Apr 2012 14:16:47 +0200 + +garlic (1.6-1) unstable; urgency=low + + * New upstream release. + + [ Michael Banck ] + * debian/control (Description): Fixed Homepage: URL, thanks to Charles + Plessy; closes: #396718. + * debian/control (XS-DM-Upload-Allowed): Added. + + [ LI Daobing ] + * debian/garlic.desktop: Fix warning for desktop-file-validate. + * debian/rules (binary/garlic): Change all script's permissions to 644. + + [ Daniel Leidert ] + * debian/compat: Raised to v5. + * debian/control: Homepage field transition. Added Vcs fields. + (Maintainer): Set the debichem team as maintainer. + (Standards-Version): Updated to latest version 3.7.3. + (Build-Depends): Raised debhelper to v5. + * debian/copyright: Fixed outdated FSF address. Fixed local reference + to point to GPL-2. + * debian/dirs: Removed (useless). + * debian/garlic.1: Fixed manpage-has-bad-whatis-entry issue + (closes: #392228). Improved the manpage slightly (applied upstream too). + * debian/garlic.desktop: Removed deprecated Encoding key. Added Chemistry + category. + * debian/menu: Updated to latest menu policy. Added longtitle. + * debian/rules: Added the langcore.mk class to determine CFLAGS. Moved all + rules and classes to the top. + (build): Tell make to override CCOPT. + (clean): Use the -f switch for rm instead to ignore the return value. + * debian/watch: Added watch file. Thanks to Justin Pryzby for his help. + * debian/patches/01_CFLAGS_fix.patch: Dropped in favour of simply giving + CCOPT via debian/rules. Added the langcore.mk class to determine CFLAGS. + + -- Michael Banck Mon, 11 Feb 2008 22:06:09 +0100 + +garlic (1.5-2) unstable; urgency=low + + * Sync with Ubuntu. + + -- Michael Banck Tue, 26 Sep 2006 00:01:48 +0200 + +garlic (1.5-1ubuntu1) edgy; urgency=low + + * Merge from debian unstable. Remaining changes: + - Added .desktop. + + -- William Alexander Grant Tue, 12 Sep 2006 14:41:15 +1000 + +garlic (1.5-1) unstable; urgency=low + + * New upstream release. + * debian/patches/01_CFLAGS_fix.patch: Updated. + * debian/control (Description): Removed Keywords, added Homepage. + + -- Michael Banck Sun, 10 Sep 2006 16:24:04 +0200 + +garlic (1.4-1ubuntu1) dapper; urgency=low + + * Add desktop file from Phill Bull (Closes Malone: #36375) + + -- Barry deFreese Sun, 9 Apr 2006 17:07:36 -0400 + +garlic (1.4-1) unstable; urgency=low + + * New upstream release; closes: #280300. + * debian/copyright: Updated download location; closes: #280301. + * debian/copyright: Updated upstream author's email address. + * debian/rules: Include simple-patchsys.mk. + * debian/patches/01_CFLAGS_fix.patch: New file. Use $(CFLAGS). This + patch was previously shipped directly in the Debian diff. + + -- Michael Banck Sat, 13 Nov 2004 17:41:54 +0100 + +garlic (1.3-3) unstable; urgency=low + + * debian/control (Build-Depends): Replace xlibs-dev with libx11-dev. + + -- Michael Banck Sun, 18 Apr 2004 04:33:40 +0200 + +garlic (1.3-2) unstable; urgency=low + + * debian/control (Build-Depends): + - Added cdbs. + - Bumped required debhelper version to (>> 4.1.0). + (Standards-Version): Bumped to 3.6.1.0. + * debian/rules: Rewritten for cdbs. + * debian/install, debian/manpages: New files. + * debian/copyright: Added note about current maintainer. + + -- Michael Banck Wed, 24 Sep 2003 20:18:10 +0200 + +garlic (1.3-1) unstable; urgency=low + + * New upstream release + * Moved menu entry from Math to Science section + * Removed debian/conffiles, debhelper takes care of /etc/garlicrc + * Don't use dh_listpackages in debian/rules, makes porting to GNU/Hurd + easier + * Bumped debhelper Build-Depends to (>> 3.0.0) + * Updated manpage + * Removed garlicrc from examples + + -- Michael Banck Sat, 5 Apr 2003 13:35:30 +0200 + +garlic (1.2-2) unstable; urgency=low + + * Fixed manpage; closes: #176632 + + -- Michael Banck Tue, 14 Jan 2003 12:39:21 +0100 + +garlic (1.2-1) unstable; urgency=low + + * New upstream release + - garlic now sends feedback upon registration; closes: #152096 + * debian/changelog: Removed emacs-variables + * debian/examples: Adjusted for new/renamed example files + * debian/control: Bumped Standards-Version: to 3.5.6.1 + + -- Michael Banck Fri, 20 Sep 2002 21:38:42 +0200 + +garlic (1.1-3) unstable; urgency=low + + * New Maintainer; closes: #151937 + * Trimmed debian/rules + * Removed debian/README.debian + * Moved menu entry into the 'math'-section in agreement with most + other visual scientific programs + * Suggests: garlic-doc, openbabel now + * debian/copyright: added note about Upstream Author + * debian/control: Changed description slightly + + -- Michael Banck Fri, 5 Jul 2002 16:32:32 +0200 + +garlic (1.1-2) unstable; urgency=low + + * Fix relative-conffile + + -- zhaoway Tue, 24 Apr 2001 07:09:13 +0800 + +garlic (1.1-1) unstable; urgency=low + + * Initial release. + + -- zhaoway Mon, 23 Apr 2001 08:19:16 +0800 + --- garlic-1.6.orig/debian/compat +++ garlic-1.6/debian/compat @@ -0,0 +1 @@ +5 --- garlic-1.6.orig/debian/manpages +++ garlic-1.6/debian/manpages @@ -0,0 +1 @@ +debian/garlic.1 --- garlic-1.6.orig/debian/copyright +++ garlic-1.6/debian/copyright @@ -0,0 +1,32 @@ +This package was debianized by zhaoway zw@debian.org on Mon, 23 Apr +2001 08:19:16 +0800. + +It is currently maintained by Michael Banck . + +It was downloaded from + +Upstream Author: Damir Zucic + +Copyright: + + Copyright (C) 2000 Damir Zucic + + This program 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, version 2. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + 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, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA + 02110-1301 USA. + +On Debian GNU systems, the complete text of the GNU General Public +License v2 can be found in `/usr/share/common-licenses/GPL-2'. + +On the world wide web A copy of the GNU General Public License is also +available at . --- garlic-1.6.orig/debian/docs +++ garlic-1.6/debian/docs @@ -0,0 +1,5 @@ +BUGS +ENVIRONMENT +HISTORY +README +TODO --- garlic-1.6.orig/debian/menu +++ garlic-1.6/debian/menu @@ -0,0 +1,7 @@ +?package(garlic):\ + needs="X11"\ + section="Applications/Science/Chemistry"\ + title="Garlic"\ + longtitle="Molecular Viewer and Editor"\ + command="/usr/bin/garlic"\ + hints="Molecular Visualization" --- garlic-1.6.orig/debian/garlic.desktop +++ garlic-1.6/debian/garlic.desktop @@ -0,0 +1,12 @@ +[Desktop Entry] +Version=1.0 +Name=Garlic Protein Visualization +Name[en_GB]=Garlic Protein Visualisation +GenericName=Protein Visualization +GenericName[en_GB]=Protein Visualisation +Comment=Visualize and investigate proteins and some geometric objects +Comment[en_GB]=Visualise and investigate proteins and some geometric objects +Type=Application +Exec=garlic +Icon=garlic +Categories=Science;Biology;Chemistry;Education; --- garlic-1.6.orig/debian/watch +++ garlic-1.6/debian/watch @@ -0,0 +1,6 @@ +# See uscan(1) for format + +version=3 +opts=downloadurlmangle=s/([^\/]+)$/$1\/$1.tar.gz/,filenamemangle=s/.*\/garlic-([\d\.]+)/garlic-$1.tar.gz/ \ + http://www.zucic.org/garlic/download/index.html \ + http://www.zucic.org/sources/garlic-([\d\.]+) --- garlic-1.6.orig/debian/examples +++ garlic-1.6/debian/examples @@ -0,0 +1,2 @@ +*.pdb +*.script --- garlic-1.6.orig/debian/garlic.1 +++ garlic-1.6/debian/garlic.1 @@ -0,0 +1,165 @@ +.TH "GARLIC" "1" "June 7, 2007" "" "" +.SH "NAME" +garlic \- molecular visualization program +.SH "SYNOPSIS" +.B garlic +.RB [ "true Garlic options" ] +.RB [ "X11 options" ] +.RB [ filename ] +.SH "DESCRIPTION" +This manual page briefly documents \fBgarlic\fR, a free molecular visualization +program. Extensive documentation in HTML format and sources may be found +at garlic home, +.RI < \%URL:http://garlic.mefos.hr/garlic/\% >. +Physical location: School of Medicine, University of Osijek, Croatia, Europe. +Precompiled packages for a number of GNU/Linux distributions are available. +These include Debian, SuSE, Mandriva, Linspire and a number of other distros. +The HTML documentation may be downloaded and unpacked for local use (recommended +usage). Here you can find a very short description of the program and the +list of command line options. +.PP +.B garlic +is a molecular visualization program originally written for investigation +of membrane proteins. Now it may be used to visualize and simple editing +of all proteins and molecules. This version recognizes PDB format version +2.1; see the source file \fIpdb_atom.c\fR for details about this format. +.SH "OPTIONS" +Command line options may be divided in two groups: \fBtrue (specific) garlic +options\fR and \fBX11 options\fR. Options may be given in any order. All options +and hard\-coded default values are listed in the table below. For each +parameter, the value defined through command line is used, if available. +If not, the value defined in \fI.garlicrc\fR file is used. If \fI.garlicrc\fR +file is not available, or there is no corresponding entry in this file, the +hard\-coded default value is used. The sample \fI.garlicrc\fR file included +in the original package contains the values equal to hard\-coded defaults. +.SS garlic options: +.TP +.B \-h, \-\-help +Print help and exit. +.TP +.B \-v, \-\-version +Print version and exit. +.TP +.B \-r, \-\-register +Register garlic: inform author that your site has garlic installed and +that someone is going to use this program. By registering, you are +encouraging author to continue development of garlic. You can also help +author to ensure support for further development. This option sends one +short e\-mail message, containing only the e\-mail message header and the +word 'Hi!',to <\&zucic@garlic.mefos.hr\&>. Please execute garlic \-r if you are +going to use this program. If you are not connected to the Internet, +consider sending a short message from some other system. +.TP +.B \-nosys +Hide the coordinate system icon (top left corner). +.TP +.B \-no\-control +Hide the control window (upper right corner). +.TP +.B \-stereo +Display stereo image. +.TP +.B \-slab \fImode\fB +Default slab mode. Available slab modes are: off, planar (default), +sphere, half\-sphere, cylinder and half cylinder. +.TP +.B \-fading \fImode\fB +Default color fading mode. Available modes: off, planar (default), +sphere, half\-sphere, cylinder and half cylinder. +.TP +.B \-as \fInumber\fB +Default atom drawing style (hard\-coded default: 2). +.TP +.B \-bs \fInumber\fB +Default bond drawing style (hard\-coded default: 2). +.TP +.B \-fs \fInumber\fB +Default number of color fading surfaces. Parallel planes, concentric +spheres or concentric cylinders may be used as fading surfaces. Three RGB +triplets are assigned to each surface. Surfaces are evenly spaced; at +least one and at most eight should be defined. At least three colors +(left, middle and right) are assigned to each visible atom. These three +colors are based on the position of a given atom relative to the nearest +fading surface(s) and on colors assigned to these surfaces. Colors are +combined using linear weighting. +.TP +.B \-lc \fIcolor\fB +Left color at the i\-th surface; i is between zero and seven. The color +string should be compliant with X11R5. Blue, for example, may be defined +as blue or as RGB:0000/0000/FFFF etc. For example +\-lc4 RGB:BBBB/8888/4444 defines the left color at the surface whose index +is equal to four. +.TP +.B \-mc \fIcolor\fB +Middle color at the i\-th surface. +.TP +.B \-rc \fIcolor\fB +Right color at the i\-th surface. +.TP +.B \-pc, \-\-print\-config +Print configuration data and exit. +.TP +.B \-pcn +Print cursor names to stdout and exit. +.TP +.B \-log \fIlogfile\fB +Write commands and messages to log file. The file will be created in the +current working directory. If this is not possible, log file will be +created in users home directory. +.PP +.SS X11 option: +.TP +.B \-display displayname +X server to contact. +.TP +.B \-geometry \fIgeom\fB +Window geometry (default: almost the whole screen). +.TP +.B \-bg \fIcolor\fB +Main window background color (default is black). +.TP +.B \-fg \fIcolor\fB +Main window foreground color (default: white). +.TP +.B \-fn \fIfontname\fB +Text font; (default is 10x20). +.TP +.B \-tbg \fIcolor\fB +Text background color (default is black). +.TP +.B \-tfg \fIcolor\fB +Text color (default is white). +.TP +.B \-cursor \fIcursorname\fB +Cursor name; see \fI/usr/include/X11/cursorfont.h\fR for names; remove the +XC_ prefix. +.SH "FILES" +.TP +The configuration file is searched in the following order: +.I ./.garlicrc +.br +.I ${HOME}/.garlicrc +.br +.I ${HOME}/garlic/.garlicrc +.br +.I /usr/share/garlic/.garlicrc +.br +.I /etc/garlicrc +.br +.I /usr/local/lib/garlic/.garlicrc +.br +.I /usr/lib/garlic/.garlicrc +.SH "SEE ALSO" +The program is fully documented in the +.I garlic\-doc +package available on Debian GNU/Linux system. +.PP +There is also documentation online at +.RI < \%URL:http://garlic.mefos.hr/garlic/docs.html\% > +.SH "AUTHOR" +.B garlic +was written by \fBDamir Zucic\fR <\&zucic@garlic.mefos.hr\&>, University of Osijek, +Croatia, Europe. +.PP +The original man page was written by \fBzhaoway\fR <\&zw@debian.org\&>, for +the Debian GNU system and later modified by \fBDamir Zucic\fR.