Author: moeller Date: 2011-05-08 13:58:38 +0000 (Sun, 08 May 2011) New Revision: 6792
Added: trunk/packages/rosetta/ trunk/packages/rosetta/trunk/ trunk/packages/rosetta/trunk/debian/ trunk/packages/rosetta/trunk/debian/README.Debian trunk/packages/rosetta/trunk/debian/README.source trunk/packages/rosetta/trunk/debian/changelog trunk/packages/rosetta/trunk/debian/compat trunk/packages/rosetta/trunk/debian/control trunk/packages/rosetta/trunk/debian/copyright trunk/packages/rosetta/trunk/debian/docs trunk/packages/rosetta/trunk/debian/patches/ trunk/packages/rosetta/trunk/debian/patches/builddoc.patch trunk/packages/rosetta/trunk/debian/patches/pdbinfo.patch trunk/packages/rosetta/trunk/debian/patches/series trunk/packages/rosetta/trunk/debian/rosetta.dirs trunk/packages/rosetta/trunk/debian/rules trunk/packages/rosetta/trunk/debian/source/ trunk/packages/rosetta/trunk/debian/source/format Log: Added build instructions for non-redistributable (and barely downloadable) but highly interesting package "rosetta". Property changes on: trunk/packages/rosetta/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/rosetta/trunk/debian/README.Debian =================================================================== --- trunk/packages/rosetta/trunk/debian/README.Debian (rev 0) +++ trunk/packages/rosetta/trunk/debian/README.Debian 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1,29 @@ +rosetta for Debian +------------------ + +This package needs a reviewer. The aim is not to achieve a maximal +compliance with the DFSG. It is too obvious that this must fail +without irritating the communication with the community. Instead +it needs to be ensured that the compilation is performed in a manner +best suited for the community. + +Of particular concern is the proper distinction between development +and debug packages. If it is considered helpful to have two packages, +i.e. one with debug information and the other without, then we +should provide those ... eventually. At the time speaking, since we +do not provide binary packages through the distribution anyway, please +inspect the file debian/rules and decide for debug or release builds. + +Completely unclear for the moment is the question if there should +be a -dev package or alternatively one just works on the upstream +source tree. + +The -doc package would be rather huge + $ du -sh html/ + 769M html/ +so I have commented out the respective code. How exactly the +arch-independent build would need to be separated from the +arch-dependent build when following that debhelper principle, +I have not figured out, yet. + + -- Steffen Moeller <[email protected]> Sat, 07 May 2011 16:27:53 +0200 Added: trunk/packages/rosetta/trunk/debian/README.source =================================================================== --- trunk/packages/rosetta/trunk/debian/README.source (rev 0) +++ trunk/packages/rosetta/trunk/debian/README.source 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1,13 @@ +rosetta for Debian +------------------ + +The upstream source code could profit considerably from a better integration with +regular Linux distributions: for too many external libraries are shipping with it +that are now commonly available through other sources. + +Only a single patch is applied as instructed on +https://www.rosettacommons.org/node/2263 +to complete the compilation. + +-- + Steffen Moeller <[email protected]> Added: trunk/packages/rosetta/trunk/debian/changelog =================================================================== --- trunk/packages/rosetta/trunk/debian/changelog (rev 0) +++ trunk/packages/rosetta/trunk/debian/changelog 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1,5 @@ +rosetta (3.2.1-1) UNRELEASED; urgency=low + + * Initial packaging. Never to be released. + + -- Steffen Moeller <[email protected]> Sat, 07 May 2011 16:27:53 +0200 Added: trunk/packages/rosetta/trunk/debian/compat =================================================================== --- trunk/packages/rosetta/trunk/debian/compat (rev 0) +++ trunk/packages/rosetta/trunk/debian/compat 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1 @@ +7 Added: trunk/packages/rosetta/trunk/debian/control =================================================================== --- trunk/packages/rosetta/trunk/debian/control (rev 0) +++ trunk/packages/rosetta/trunk/debian/control 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1,37 @@ +Source: rosetta +Section: non-free/science +Priority: extra +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 7.0.50~), scons +#Build-Depends-Indep: doxygen +Standards-Version: 3.9.2 +Homepage: http://www.rosettacommons.org +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rosetta/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/rosetta/trunk/ + +Package: rosetta +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: molecular biophysics for structural biology + The Rosetta software suite focuses on the prediction and design of + protein structures, protein folding mechanisms, and protein-protein + interactions. Rosetta has been consistently successful in CASP and + CAPRI competitions. Rosetta also addresses aspects of protein design, + docking and structure. The software is the foundation for the Human + Proteome Folding Project on the World Community Grid and the Roseta@home + distributed computing project. + . + The Rosetta software suite is currently licensed for free to users at + academic and nonprofit institutions. Over 2000 academic users in more + than 32 countries use Rosetta. Commercial entities can use Rosetta by + paying a license fee. Revenue from licensing is reinvested in supporting + continued software development. + +Package: rosetta-dbg +Architecture: any +Section: non-free/debug +Depends: ${shlibs:Depends}, ${misc:Depends}, rosetta +Description: debug info for rosetta molecular dynamics suite + The default build leaves debug information in. Debian has + a mechanism to extrat that into a separate file which is + then available to submit best-possible bug reports. Added: trunk/packages/rosetta/trunk/debian/copyright =================================================================== --- trunk/packages/rosetta/trunk/debian/copyright (rev 0) +++ trunk/packages/rosetta/trunk/debian/copyright 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1,38 @@ +Format: http://dep.debian.net/deps/dep5 +Upstream-Name: rosetta +Source: <url://example.com> + +Files: * +Copyright: + (c) Copyright Rosetta Commons Member Institutions. +License: non-transferable + Debian should never see the software on its servers. If you see this + software installed, you should investigate if the license is an academic + one of the commercial variant. For consequences for your research project + consult your employer, the Rosetta Commons web page and when in doubt + the contact email below. + (c) All the files in this directory and sub-directories are part of the Rosetta software + (c) suite and are made available under license. The Rosetta software is developed by the + (c) contributing members of the Rosetta Commons. For more information, see + (c) http://www.rosettacommons.org. Questions about this can be addressed to University of + (c) Washington UW TechTransfer, email: [email protected]. + + +Files: debian/* +Copyright: 2011 Steffen Moeller <[email protected]> +License: GPL-3+ + 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 3 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 3 can be found in "/usr/share/common-licenses/GPL-3". Added: trunk/packages/rosetta/trunk/debian/docs =================================================================== --- trunk/packages/rosetta/trunk/debian/docs (rev 0) +++ trunk/packages/rosetta/trunk/debian/docs 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1,3 @@ +README.Copyrights +readme.txt +README.version Added: trunk/packages/rosetta/trunk/debian/patches/builddoc.patch =================================================================== --- trunk/packages/rosetta/trunk/debian/patches/builddoc.patch (rev 0) +++ trunk/packages/rosetta/trunk/debian/patches/builddoc.patch 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1,21 @@ +Index: rosetta-3.2.1/BuildDocs.sh +=================================================================== +--- rosetta-3.2.1.orig/BuildDocs.sh 2011-05-07 21:37:47.000000000 +0200 ++++ rosetta-3.2.1/BuildDocs.sh 2011-05-07 21:38:28.000000000 +0200 +@@ -1,9 +1,15 @@ + #!/bin/bash + ++set -x ++set -e ++ + echo 'Building documentation for each src/doxygen.*' + + mkdir html +-cp doc/index.html html/ ++ ++if [ -r doc/index.html ]; then ++ cp doc/index.html html/ ++fi + + rm -rf html/core+protocols html/all_else + Added: trunk/packages/rosetta/trunk/debian/patches/pdbinfo.patch =================================================================== --- trunk/packages/rosetta/trunk/debian/patches/pdbinfo.patch (rev 0) +++ trunk/packages/rosetta/trunk/debian/patches/pdbinfo.patch 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1,13 @@ +Index: rosetta-3.2.1/src/core/conformation/symmetry/util.cc +=================================================================== +--- rosetta-3.2.1.orig/src/core/conformation/symmetry/util.cc 2011-05-07 17:16:48.000000000 +0200 ++++ rosetta-3.2.1/src/core/conformation/symmetry/util.cc 2011-05-07 17:17:49.000000000 +0200 +@@ -357,7 +357,7 @@ + #ifdef WIN32 + pose::PDBInfoOP pdb_info_src (new pose::PDBInfo( pose.pdb_info() )); + #else +- pose::PDBInfoOP pdb_info_src = new pose::PDBInfo::PDBInfo( pose.pdb_info() ); ++ pose::PDBInfoOP pdb_info_src = new pose::PDBInfo( pose.pdb_info() ); + #endif + + if ( !pose.pdb_info() ) Added: trunk/packages/rosetta/trunk/debian/patches/series =================================================================== --- trunk/packages/rosetta/trunk/debian/patches/series (rev 0) +++ trunk/packages/rosetta/trunk/debian/patches/series 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1,2 @@ +pdbinfo.patch +builddoc.patch Added: trunk/packages/rosetta/trunk/debian/rosetta.dirs =================================================================== --- trunk/packages/rosetta/trunk/debian/rosetta.dirs (rev 0) +++ trunk/packages/rosetta/trunk/debian/rosetta.dirs 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1,3 @@ +usr/lib/rosetta/bin +usr/lib/rosetta/lib +usr/bin Added: trunk/packages/rosetta/trunk/debian/rules =================================================================== --- trunk/packages/rosetta/trunk/debian/rules (rev 0) +++ trunk/packages/rosetta/trunk/debian/rules 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1,36 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# Sample debian/rules that uses debhelper. + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +#override_dh_auto_build: +override_dh_auto_build: + #scons cxx=gcc mode=release cxx_ver=4.4 -j 12 bin + scons cxx=gcc cxx_ver=4.4 -j 12 bin + #./BuildDocs.sh + +override_dh_install: + # retrieving everything from symbolik link + cp -r -L bin/* $(CURDIR)/debian/rosetta/usr/lib/rosetta/bin/ + # leaving object files, copying libraries + find build -name "lib*" | xargs -r cp -t $(CURDIR)/debian/rosetta/usr/lib/rosetta/lib + # arranging for non-obvious location of library, substituting previous rpath setting + chrpath -r /usr/lib/rosetta/lib $(CURDIR)/debian/rosetta/usr/lib/rosetta/bin/* + + # placing symbolic links to executables + cd $(CURDIR)/debian/rosetta/usr/bin ; \ + for i in `find $(CURDIR)/debian/rosetta/usr/lib/rosetta/bin | grep -v .default.` ; \ + do \ + b=`basename $$i` ; \ + d=`echo $$b | sed -e 's/\..*//'` ; \ + ln -sf ../lib/rosetta/bin/$$b "$$d"; \ + done + +override_dh_strip: + dh_strip --dbg-package rosetta-dbg + + +%: + dh $@ Property changes on: trunk/packages/rosetta/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/rosetta/trunk/debian/source/format =================================================================== --- trunk/packages/rosetta/trunk/debian/source/format (rev 0) +++ trunk/packages/rosetta/trunk/debian/source/format 2011-05-08 13:58:38 UTC (rev 6792) @@ -0,0 +1 @@ +3.0 (quilt) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
