[med-svn] r6792 - in trunk/packages: . rosetta rosetta/trunk rosetta/trunk/debian rosetta/trunk/debian/patches rosetta/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Sun May 8 13:58:43 UTC 2011
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 <moeller at debian.org> 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 <moeller at debian.org>
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 <moeller at debian.org> 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 <moeller at debian.org>
+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 at 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: license at u.washington.edu.
+
+
+Files: debian/*
+Copyright: 2011 Steffen Moeller <moeller at debian.org>
+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)
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