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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +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 <[email protected]> + +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 ([email protected]) 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 + ([email protected]) 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 [email protected] + for a copy). + + UNDERSTOOD AND AGREED. + + + Contact Information: + + The best contact path for licensing issues is by e-mail to + [email protected] 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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
