[med-svn] r6162 - in trunk/packages: . vmd vmd/trunk vmd/trunk/debian vmd/trunk/debian/patches vmd/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Sat Mar 5 13:45:35 UTC 2011
Author: moeller
Date: 2011-03-05 13:45:34 +0000 (Sat, 05 Mar 2011)
New Revision: 6162
Added:
trunk/packages/vmd/
trunk/packages/vmd/trunk/
trunk/packages/vmd/trunk/debian/
trunk/packages/vmd/trunk/debian/README.Debian
trunk/packages/vmd/trunk/debian/README.source
trunk/packages/vmd/trunk/debian/changelog
trunk/packages/vmd/trunk/debian/compat
trunk/packages/vmd/trunk/debian/control
trunk/packages/vmd/trunk/debian/copyright
trunk/packages/vmd/trunk/debian/patches/
trunk/packages/vmd/trunk/debian/patches/plugins_build.patch
trunk/packages/vmd/trunk/debian/patches/series
trunk/packages/vmd/trunk/debian/rules
trunk/packages/vmd/trunk/debian/source/
trunk/packages/vmd/trunk/debian/source/format
trunk/packages/vmd/trunk/debian/vmd.docs
Log:
First shot at VMD.
Property changes on: trunk/packages/vmd/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/vmd/trunk/debian/README.Debian
===================================================================
--- trunk/packages/vmd/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/vmd/trunk/debian/README.Debian 2011-03-05 13:45:34 UTC (rev 6162)
@@ -0,0 +1,14 @@
+vmd for Debian
+--------------
+
+This package will not be shipped with the Debian main servers.
+It shall only help to identify the build dependencies and
+gather ideas on how to e.g. cater for build requirements for
+CUDA and OpenCL libraries.
+
+Another motivation for packaging VMD is to help upstream
+to identify our distribution as a source for valuable technical
+feedback. Eventually this source directory is likely to move
+over to Debian Science.
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 05 Mar 2011 12:38:44 +0100
Added: trunk/packages/vmd/trunk/debian/README.source
===================================================================
--- trunk/packages/vmd/trunk/debian/README.source (rev 0)
+++ trunk/packages/vmd/trunk/debian/README.source 2011-03-05 13:45:34 UTC (rev 6162)
@@ -0,0 +1,11 @@
+vmd for Debian
+--------------
+
+VMD will not be redistributed.
+
+ * all CVS directories where removed from the sources
+ * the plugin directory was moved into the vmd-$(version)
+ folder
+
+
+
Added: trunk/packages/vmd/trunk/debian/changelog
===================================================================
--- trunk/packages/vmd/trunk/debian/changelog (rev 0)
+++ trunk/packages/vmd/trunk/debian/changelog 2011-03-05 13:45:34 UTC (rev 6162)
@@ -0,0 +1,7 @@
+vmd (1.9~beta2-1) UNRELEASED; urgency=low
+
+ * This package only serves the better communication among
+ Debian users of the package. Its current license does not
+ allow the redistribution of the source or binaries.
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 05 Mar 2011 14:27:03 +0100
Added: trunk/packages/vmd/trunk/debian/compat
===================================================================
--- trunk/packages/vmd/trunk/debian/compat (rev 0)
+++ trunk/packages/vmd/trunk/debian/compat 2011-03-05 13:45:34 UTC (rev 6162)
@@ -0,0 +1 @@
+7
Added: trunk/packages/vmd/trunk/debian/control
===================================================================
--- trunk/packages/vmd/trunk/debian/control (rev 0)
+++ trunk/packages/vmd/trunk/debian/control 2011-03-05 13:45:34 UTC (rev 6162)
@@ -0,0 +1,25 @@
+Source: vmd
+Section: non-free/science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 7.0.50~), autotools-dev, tcl8.5-dev
+Standards-Version: 3.9.1
+Homepage: http://www.ks.uiuc.edu/Research/vmd/
+#Vcs-Git: git://git.debian.org/collab-maint/vmd.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/vmd.git;a=summary
+
+Package: vmd
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: presentation of traces of molecular dynamics runs
+ VMD stands for Visual Molecular Dynamics. While text books
+ and even structure databases because of technical problems only
+ present static pictures of proteins or DNA, for the understanding
+ of the properties of those molecules their vibration or their
+ movement in general is important.
+ .
+ The movements itself are calculated by molecular dynamics programs,
+ such as NAMD (by the same group), Rosetta, BALLView or GROMACS. The
+ latter two are already in the distribution. VMD has a series of
+ nice features, from displaying through animation to analysing.
+ It can be scripted, clustered, and runs on all common OS.
Added: trunk/packages/vmd/trunk/debian/copyright
===================================================================
--- trunk/packages/vmd/trunk/debian/copyright (rev 0)
+++ trunk/packages/vmd/trunk/debian/copyright 2011-03-05 13:45:34 UTC (rev 6162)
@@ -0,0 +1,172 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: vmd
+Source: http://www.ks.uiuc.edu/Research/vmd/
+
+Files: *
+Copyright: 2000-2011 VMD Team <vmd at ks.uiuc.edu>
+
+License:
+ UNIVERSITY OF ILLINOIS
+ VISUAL MOLECULAR DYNAMICS SOFTWARE LICENSE AGREEMENT
+
+ Upon execution of this Agreement by the party identified below
+ ("Licensee"), The Board of Trustees of the University of Illinois
+ ("Illinois"), on behalf of The Theoretical and Computational
+ Biophysics Group ("TCBG") in the Beckman Institute, will provide the
+ Visual Molecular Dynamics ("VMD") software in ExecutableCode and/or
+ Source Code form ("Software") to Licensee, subject to the following
+ terms and conditions. For purposes of this Agreement, Executable
+ Code is the compiled code, which is ready to run on Licensee's
+ computer. Source code consists of a set of files which contain the
+ actual program commands that are compiled to form the Executable Code.
+
+ 1. The Software is intellectual property owned by Illinois,
+ and all right, title and interest, including copyright, remain
+ with Illinois. Illinois grants, and Licensee hereby accepts,
+ a restricted, non-exclusive, non-transferable license to use the
+ Software for academic, research and internal business purposes only,
+ e.g. not for commercial use (see Clause 7 below), without a fee.
+
+ 2. Licensee may, at its own expense, create and freely distribute
+ complimentary works that interoperate with the Software, directing
+ others to the TCBG server to license and obtain the Software
+ itself. Licensee may, at its own expense, modify the Software
+ to make derivative works. Except as explicitly provided below,
+ this License shall apply to any derivative work as it does to the
+ original Software distributed by Illinois. Any derivative work
+ should be clearly marked and renamed to notify users that it is
+ a modified version and not the original Software distributed by
+ Illinois. Licensee agrees to reproduce the copyright notice and
+ other proprietary markings on any derivative work and to include in
+ the documentation of such work the acknowledgement:
+
+ "This software includes code developed by the Theoretical and
+ Computational Biophysics Group in the Beckman Institute for Advanced
+ Science and Technology at the University of Illinois at Urbana-Champaign."
+
+ Licensee may redistribute without restriction works with up to
+ 1/2 of their non-comment source code derived from at most 1/10 of
+ the non-comment source code developed by Illinois and contained
+ in the Software, provided that the above directions for notice and
+ acknowledgement are observed. Any other distribution of the Software
+ or any derivative work requires a separate license with Illinois.
+ Licensee may contact Illinois (vmd at ks.uiuc.edu) to negotiate an
+ appropriate license for such distribution.
+
+ 3. Except as expressly set forth in this Agreement, THIS SOFTWARE IS
+ PROVIDED "AS IS" AND ILLINOIS MAKES NO REPRESENTATIONS AND EXTENDS
+ NO WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING
+ BUT NOT LIMITED TO WARRANTIES OR MERCHANTABILITY OR FITNESS FOR
+ A PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT
+ INFRINGE ANY PATENT, TRADEMARK, OR OTHER RIGHTS. LICENSEE ASSUMES
+ THE ENTIRE RISK AS TO THE RESULTS AND PERFORMANCE OF THE SOFTWARE
+ AND/OR ASSOCIATED MATERIALS. LICENSEE AGREES THAT UNIVERSITY
+ SHALL NOT BE HELD LIABLE FOR ANY DIRECT,INDIRECT, CONSEQUENTIAL,
+ OR INCIDENTAL DAMAGES WITH RESPECT TO ANY CLAIM BY LICENSEE OR ANY
+ THIRD PARTY ON ACCOUNT OF OR ARISING FROM THIS AGREEMENT OR USE OF
+ THE SOFTWARE AND/OR ASSOCIATED MATERIALS.
+
+ 4. Licensee understands the Software is proprietary to
+ Illinois. Licensee agrees to take all reasonable steps to insure
+ that the Softwareis protected and secured from unauthorized
+ disclosure, use, or release and will treat it with at least the
+ same level of care as Licensee would use to protect and secure its
+ own proprietary computer programs and/or information, but using no
+ less than a reasonable standard of care. Licensee agrees to provide
+ the Software only to any other person or entity who has registered
+ with Illinois. If licensee is not registering as an individual but
+ as an institution or corporation each member of the institution or
+ corporation who has access to or uses Software must agree to and
+ abide by the terms of this license. If Licensee becomes aware of
+ any unauthorized licensing, copying or use of the Software, Licensee
+ shall promptly notify Illinois in writing. Licensee expressly agrees
+ to use the Software only in the manner and for the specific uses
+ authorized in this Agreement.
+
+ 5. By using or copying this Software, Licensee agrees to abide
+ by the copyright law and all other applicable laws of the
+ U.S. including, but not limited to, export control laws and the
+ terms of this license. Illinois shall have the right to terminate
+ this license immediately by written notice upon Licensee's breach
+ of, or non-compliance with, any terms of the license. Licensee may
+ be held legally responsible for any copyright infringement that is
+ caused or encouraged by its failure to
+ abideby the terms of this license. Upon termination, Licensee
+ agrees to
+ destroyall copies of the Software in its possession and to verify
+ such destruction in writing.
+
+ 6. The user agrees that any reports or published results obtained
+ with the Software will acknowledge its use by the appropriate citation
+ as follows:
+
+ "VMD was developed by the Theoretical and Computational Biophysics Group
+ in the Beckman Institute for Advanced Science and Technology at the
+ University of Illinois at Urbana-Champaign."
+
+ Any published work which utilizes VMD shall include the following reference:
+ "Humphrey, W., Dalke, A. and Schulten, K., `VMD -Visual Molecular
+ Dynamics', J. Molecular Graphics, 1996, vol. 14, pp. 33-38."
+
+ Electronic documents will include a direct link to the official VMD page
+ at http://www.ks.uiuc.edu/Research/vmd/
+
+ 7. Commercial use of the Software, or derivative works based
+ thereon, REQUIRES A COMMERCIAL LICENSE. Should Licensee wish to
+ make commercial use of the Software, Licensee will contact Illinois
+ (vmd at ks.uiuc.edu) to negotiate an appropriate license for such
+ use. Commercial use includes: (1) integration of all or part of the
+ Software into a product for sale, lease or license by or on behalf
+ of Licensee to third parties, or (2) distribution of the Software to
+ third parties that need it to commercialize product sold or licensed
+ by or on behalf of Licensee.
+
+ 8. Government Rights. Because substantial governmental funds have been
+ used in the development of VMD, any possession, use or sublicense of
+ the Software by or to the United States government shall be subject
+ to such required restrictions.
+
+ 9. VMD is being distributed as a research and teaching tool and as
+ such, TCBG encourages contributions from users of the code that
+ might, at Illinois' sole discretion, be used or incorporated to
+ make the basic operating framework of the Software a more stable,
+ flexible, and/or useful product. Licensees who contribute their code
+ to become an internal portion of the Software agree that such code
+ may be distributed by Illinois under the terms of this License and
+ may be required to sign an "Agreement Regarding Contributory Code for
+ VMD Software" before Illinois can accept it (contact vmd at ks.uiuc.edu
+ for a copy).
+
+ UNDERSTOOD AND AGREED.
+
+
+ Contact Information:
+
+ The best contact path for licensing issues is by e-mail to
+ vmd at ks.uiuc.edu or send correspondence to:
+ VMD Team
+ Theoretical and Computational Biophysics Group
+ Beckman Institute
+ University of Illinois
+ 405 North Mathews MC-251
+ Urbana, Illinois 61801 USA
+ FAX: (217) 244-6078
+
+Files: debian/*
+Copyright: 2011 Steffen Moeller <moeller at debian.org>
+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
+ (at your option) any later version.
+ .
+ This package 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, 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".
Added: trunk/packages/vmd/trunk/debian/patches/plugins_build.patch
===================================================================
--- trunk/packages/vmd/trunk/debian/patches/plugins_build.patch (rev 0)
+++ trunk/packages/vmd/trunk/debian/patches/plugins_build.patch 2011-03-05 13:45:34 UTC (rev 6162)
@@ -0,0 +1,34 @@
+Index: plugins_source/build.csh
+===================================================================
+--- vmd-1.9~beta2.orig/plugins_source/build.csh 2011-03-05 13:59:24.960662569 +0100
++++ vmd-1.9~beta2/plugins_source/build.csh 2011-03-05 14:01:56.176662571 +0100
+@@ -184,21 +184,18 @@
+ echo "Plugin builds done..."
+ breaksw;
+
+-
+ ###
+ ### XXXNEWPLATFORM
+ ###
+ default:
+- echo "Unrecognized host system, add your own switch statement to customize"
+- echo "for your build environment. Edit build.csh and change the variables"
+- echo "in the section marked XXXNEWPLATFORM."
+- # setenv TCLINC -I/your/tcl/include/directory
+- # setenv TCLLIB -L/your/tcl/library/directory
+- # cd $unixdir; gmake LINUX TCLINC=$TCLINC TCLLIB=$TCLLIB/lib_LINUX >& log.LINUX.$DATE < /dev/null &
+- # echo "Waiting for all plugin make jobs to complete..."
+- # wait;
+- # echo ""
+- # echo "Plugin builds done..."
++ echo "Building on Debian Linux"
++ setenv TCLINC -I/usr/include/tcl
++ setenv TCLLIB -L/usr/lib
++ cd $unixdir; make LINUX TCLINC=$TCLINC TCLLIB=$TCLLIB/lib_LINUX >& log.LINUX.$DATE < /dev/null &
++ echo "Waiting for all plugin make jobs to complete..."
++ wait;
++ echo ""
++ echo "Plugin builds done..."
+ breaksw;
+ endsw
+
Added: trunk/packages/vmd/trunk/debian/patches/series
===================================================================
--- trunk/packages/vmd/trunk/debian/patches/series (rev 0)
+++ trunk/packages/vmd/trunk/debian/patches/series 2011-03-05 13:45:34 UTC (rev 6162)
@@ -0,0 +1 @@
+plugins_build.patch
Added: trunk/packages/vmd/trunk/debian/rules
===================================================================
--- trunk/packages/vmd/trunk/debian/rules (rev 0)
+++ trunk/packages/vmd/trunk/debian/rules 2011-03-05 13:45:34 UTC (rev 6162)
@@ -0,0 +1,35 @@
+#!/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
+
+ifeq (Linux,$(shell uname -s))
+KERNEL=LINUX
+else
+KERNEL="--help unknown_kernel "
+endif
+ifeq (x86_64,$(shell uname -m))
+PLATFORM=AMD64
+else
+PLATFORM=" --help unknown_machine"
+endif
+
+%:
+ dh $@
+
+override_dh_auto_configure:
+ #FREEBSD FREEBSDAMD64 HPUX11 AIX4 AIX5 AIX5_64 AIX6_64 BLUEWATERS LINUX LINUXALPHA LINUXAMD64 LINUXIA64 LINUXPPC LINUXPPC64 MACOSX MACOSXX86 MACOSXX86_64 TRU64 SOLARIS2 SOLARIS2_64 SOLARISX86 SOLARISX86_64 WIN32 WIN64)
+ echo "Compiling plugins first"
+ cd plugins_source && ./build.csh
+ cd plugins_source && PLUGINDIR=../plugins make distrib
+ echo "Now configuring core VMD"
+ ./configure $(KERNEL)$(PLATFORM)
+
+override_dh_auto_build:
+ cd src && make veryclean && make
Property changes on: trunk/packages/vmd/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/vmd/trunk/debian/source/format
===================================================================
--- trunk/packages/vmd/trunk/debian/source/format (rev 0)
+++ trunk/packages/vmd/trunk/debian/source/format 2011-03-05 13:45:34 UTC (rev 6162)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/vmd/trunk/debian/vmd.docs
===================================================================
--- trunk/packages/vmd/trunk/debian/vmd.docs (rev 0)
+++ trunk/packages/vmd/trunk/debian/vmd.docs 2011-03-05 13:45:34 UTC (rev 6162)
@@ -0,0 +1 @@
+README
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