[med-svn] r1096 - in trunk/packages: . btk-core btk-core/trunk btk-core/trunk/debian btk-core/trunk/debian/patches

tille at alioth.debian.org tille at alioth.debian.org
Thu Jan 10 15:57:49 UTC 2008


Author: tille
Date: 2008-01-10 15:57:48 +0000 (Thu, 10 Jan 2008)
New Revision: 1096

Added:
   trunk/packages/btk-core/
   trunk/packages/btk-core/trunk/
   trunk/packages/btk-core/trunk/debian/
   trunk/packages/btk-core/trunk/debian/changelog
   trunk/packages/btk-core/trunk/debian/compat
   trunk/packages/btk-core/trunk/debian/control
   trunk/packages/btk-core/trunk/debian/copyright
   trunk/packages/btk-core/trunk/debian/docs
   trunk/packages/btk-core/trunk/debian/libbtk-core-dev.examples
   trunk/packages/btk-core/trunk/debian/libbtk-core-dev.install
   trunk/packages/btk-core/trunk/debian/patches/
   trunk/packages/btk-core/trunk/debian/patches/00list
   trunk/packages/btk-core/trunk/debian/patches/100-Makefile.am.dpatch
   trunk/packages/btk-core/trunk/debian/patches/100-btk_core_Makefile.am.dpatch
   trunk/packages/btk-core/trunk/debian/rmsd.1
   trunk/packages/btk-core/trunk/debian/rules
   trunk/packages/btk-core/trunk/debian/transform_structure.1
   trunk/packages/btk-core/trunk/debian/watch
Log:
Added btk-core


Added: trunk/packages/btk-core/trunk/debian/changelog
===================================================================
--- trunk/packages/btk-core/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/changelog	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,17 @@
+btk-core (0.8.1-1) unstable; urgency=low
+
+  * Modified for upload to Debian (Closes #459753)
+  * Use standards versions 3.7.3
+  
+ -- Morten Kjeldgaard <mok at bioxray.dk>  Tue, 08 Jan 2008 15:22:01 +0100
+
+btk-core (0.8.1-0ubuntu1) gutsy; urgency=low
+
+  * Initial release. 
+  * Authored man pages rmsd.1 and transform_structure.1; these 
+    can be found along with the code examples.
+  * Patched automake files to install in $(DESTDIR) and to disable
+    install-hooks that would delete files in /usr. Therefore,
+    rules needs to call aclocal & friends.
+
+ -- Morten Kjeldgaard <mok at bioxray.dk>  Fri, 17 Aug 2007 14:17:43 +0200

Added: trunk/packages/btk-core/trunk/debian/compat
===================================================================
--- trunk/packages/btk-core/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/compat	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1 @@
+5

Added: trunk/packages/btk-core/trunk/debian/control
===================================================================
--- trunk/packages/btk-core/trunk/debian/control	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/control	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,19 @@
+Source: btk-core
+Section: science
+Priority: optional
+Maintainer: Morten Kjeldgaard <mok at bioxray.dk>
+Homepage: http://sourceforge.net/projects/btk/  
+Build-Depends: debhelper (>= 5), dpatch, automake, libboost-dev
+Standards-Version: 3.7.3
+
+Package: libbtk-core-dev
+Architecture: any
+Depends: libboost-dev 
+Description: Biomolecule Toolkit C++ library
+ The Biomolecule Toolkit is a library for modeling biological
+ macromolecules such as proteins, DNA and RNA. It provides a C++ interface
+ for common tasks in structural biology to facilitate the development of
+ molecular modeling, design and analysis tools.
+ .
+ This package contains header files and libraries necessary to develop 
+ programs using the Biomolecular Toolkit.

Added: trunk/packages/btk-core/trunk/debian/copyright
===================================================================
--- trunk/packages/btk-core/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/copyright	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,36 @@
+This package was debianized by Morten Kjeldgaard <mok at bioxray.dk> on
+Sun, 10 Jun 2007 16:13:07 +0000.
+
+
+The source code for the Biomolecule Toolkit was downloaded from
+http://sourceforge.net/projects/btk/
+
+Upstream Authors:
+    Tim Robertson (kid50 at users.sourceforge.net>
+    Chris Saunders (ctsa at users.sourceforge.net>
+
+Copyright: 2006 Tim Robertson, Chris Saunders, Alex Morozov, Eric Alm &
+    Jeff Gray
+
+License:
+
+    This package is free software; you can redistribute it and/or
+    modify it under the terms of the GNU Lesser General Public
+    License as published by the Free Software Foundation; either
+    version 2.1 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
+    Lesser General Public License for more details.
+
+    You should have received a copy of the GNU Lesser General Public
+    License along with this package; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+
+On Debian systems, the complete text of the GNU Lesser General
+Public License can be found in `/usr/share/common-licenses/LGPL-2.1'.
+
+
+The Debian packaging is (C) 2007, Morten Kjeldgaard <mok at bioxray.dk> and
+is licensed under the LGPL version 2.1, like the toolkit itself.

Added: trunk/packages/btk-core/trunk/debian/docs
===================================================================
--- trunk/packages/btk-core/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/docs	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,3 @@
+NEWS
+README
+HACKING

Added: trunk/packages/btk-core/trunk/debian/libbtk-core-dev.examples
===================================================================
--- trunk/packages/btk-core/trunk/debian/libbtk-core-dev.examples	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/libbtk-core-dev.examples	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,3 @@
+examples/*.cpp
+debian/rmsd.1
+debian/transform_structure.1

Added: trunk/packages/btk-core/trunk/debian/libbtk-core-dev.install
===================================================================
--- trunk/packages/btk-core/trunk/debian/libbtk-core-dev.install	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/libbtk-core-dev.install	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,2 @@
+usr/include/btk
+usr/lib

Added: trunk/packages/btk-core/trunk/debian/patches/00list
===================================================================
--- trunk/packages/btk-core/trunk/debian/patches/00list	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/patches/00list	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,2 @@
+100-Makefile.am.dpatch
+100-btk_core_Makefile.am.dpatch

Added: trunk/packages/btk-core/trunk/debian/patches/100-Makefile.am.dpatch
===================================================================
--- trunk/packages/btk-core/trunk/debian/patches/100-Makefile.am.dpatch	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/patches/100-Makefile.am.dpatch	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,20 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 100-Makefile.am.dpatch by Morten Kjeldgaard <mok at bioxray.dk>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Remove the uninstall-hook in top level Makefile.am
+
+ at DPATCH@
+diff -urNad btk-core-0.8~/Makefile.am btk-core-0.8/Makefile.am
+--- btk-core-0.8~/Makefile.am	2007-06-21 18:49:04.000000000 +0000
++++ btk-core-0.8/Makefile.am	2007-06-21 18:49:42.000000000 +0000
+@@ -1,7 +1,4 @@
+ EXTRA_DIST = ChangeLog AUTHORS COPYING HACKING INSTALL NEWS README
+ 
+ SUBDIRS = btk tests examples
+-
+-uninstall-hook:
+-	(cd $(libdir) && if [ ! `ls -A btk` ] ; then rmdir btk; fi)
+-	(cd $(includedir) && if [ ! `ls -A btk` ] ; then rmdir btk; fi) 
+\ No newline at end of file
++ACLOCAL_AMFLAGS = -I btk/core/config

Added: trunk/packages/btk-core/trunk/debian/patches/100-btk_core_Makefile.am.dpatch
===================================================================
--- trunk/packages/btk-core/trunk/debian/patches/100-btk_core_Makefile.am.dpatch	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/patches/100-btk_core_Makefile.am.dpatch	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,35 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 100-btk_core_Makefile.am.dpatch by Morten Kjeldgaard <mok at bioxray.dk>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Use $DESTDIR in this Makefile.am
+
+ at DPATCH@
+--- foo/btk/core/Makefile.am	2006-10-27 02:37:24.000000000 +0000
++++ foo/btk/core/Makefile.am.new	2007-06-10 16:51:49.000000000 +0000
+@@ -85,16 +85,17 @@
+ math/vector_math.cpp \
+ algorithms/rmsd.cpp
+ 
++
+ install-exec-hook:
+-	if [ -e $(pkglibdir)/libbtk_core.a ]; \
+-	then rm -f $(pkglibdir)/libbtk_core.a; fi
+-	cd $(pkglibdir) && @LN_S@ libbtk_core_ at VERSION@.a libbtk_core.a
++	if [ -e $(DESTDIR)/$(pkglibdir)/libbtk_core.a ]; \
++	then rm -f $(DESTDIR)/$(pkglibdir)/libbtk_core.a; fi
++	cd $(DESTDIR)/$(pkglibdir) && @LN_S@ libbtk_core_ at VERSION@.a libbtk_core.a
+ 
+ install-data-hook:
+-	if [ -e $(includedir)/btk/core ]; \
+-	then rm -f $(includedir)/btk/core; fi
+-	cd $(includedir)/btk && @LN_S@ @PACKAGE at _@VERSION@ core
++	if [ -e $(DESTDIR)/$(includedir)/btk/core ]; \
++	then rm -f $(DESTDIR)/$(includedir)/btk/core; fi
++	cd $(DESTDIR)/$(includedir)/btk && @LN_S@ @PACKAGE at _@VERSION@ core
+ 
+ uninstall-hook:
+-	cd $(pkglibdir) && rm -f libbtk_core.a
+-	cd $(includedir)/btk && rm -fr core @PACKAGE at _@VERSION@
++	cd $(DESTDIR)/$(pkglibdir) && rm -f libbtk_core.a
++	cd $(DESTDIR)/$(includedir)/btk && rm -fr core @PACKAGE at _@VERSION@

Added: trunk/packages/btk-core/trunk/debian/rmsd.1
===================================================================
--- trunk/packages/btk-core/trunk/debian/rmsd.1	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/rmsd.1	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,53 @@
+.\"   Hey, EMACS: -*- mode: nroff; mode: font-lock -*-
+.TH RMSD 1 "June 2007" "User Commands"
+.SH NAME
+rmsd \- calculate optimal superposition of two PDB structures
+.SH DESCRIPTION
+usage: \fBrmsd\fR \fB\-pdb1\fR pdb_file1 \fB\-pdb2\fR pdb_file2 [options]
+.PP
+Calculates the optimal superposition of the structure in \fIpdb_file2\fR to
+the structure in \fIpdb_file1\fR.  Reports the root mean square deviation
+between corresponding atoms in the two structures.  By default, all
+non\-heterogen atoms in the structures are aligned.
+.SH OPTIONS
+.SS Selection options
+.TP
+\fB\-pdb1_chain\fR \fI<chain id>\fR  
+specify a chain to use in pdb_file1
+.TP
+\fB\-pdb2_chain\fR \fI<chain id>\fR 
+specify a chain to use in pdb_file2
+.TP
+\fB\-bb\fR              
+select protein backbone atoms
+.TP
+\fB\-calpha\fR          
+select C\-alpha atoms
+.TP
+\fB\-start\fR \fI<N>\fR       
+select atoms with residue number higher than N.
+.TP
+\fB\-stop\fR \fI<N>\fR       
+ select atoms with residue number lower than N.
+.TP
+\fB\-hetatoms\fR 
+include hetatoms in alignment (default: exclude hetatoms)
+.PP
+The union of multiple selection options is used.
+.SS Output options:
+.TP
+\fB\-pdb2_out\fR \fI<file>\fR       
+output a copy of pdb2, in its optimal superposition to pdb1
+.TP
+\fB\-pdb2_trans_out\fR \fI<file>\fR
+write to file the rotation R and translation T that superimpose
+the selected atoms of pdb2 to those of pdb1
+
+.SH "SEE ALSO"
+.B transform_structure
+(1)
+.SH AUTHORS
+\fBrmsd\fR was written by the BTK project (http://projects.sf.net/btk)
+.PP
+This manual page was written for the Ubuntu project by Morten Kjeldgaard
+<mok at bioxray.dk>

Added: trunk/packages/btk-core/trunk/debian/rules
===================================================================
--- trunk/packages/btk-core/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/rules	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,106 @@
+#!/usr/bin/make -f
+# -*- mode: makefile; mode: font-lock -*-
+#
+# 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.
+#
+# Modified to make a template file for a multi-binary package with separated
+# build-arch and build-indep targets  by Bill Allombert 2001
+# Modified to build btk-core package by Morten Kjeldgaard June, 2007
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# This has to be exported to make some magic below work.
+export DH_OPTIONS
+
+# These are used for cross-compiling and for saving the configure script
+# from having to guess our platform (since we know it already)
+DEB_HOST_GNU_TYPE   ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DEB_BUILD_GNU_TYPE  ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+include /usr/share/dpatch/dpatch.make
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+	CFLAGS += -O0
+else
+	CFLAGS += -O2
+endif
+
+config.status: patch-stamp configure
+	dh_testdir
+
+	./configure --host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info --with-boost=/usr/include/boost CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs"
+
+configure: configure.ac
+	dh_testdir
+	aclocal -I btk/core/config
+	automake
+	autoconf
+
+#Architecture 
+build: build-arch 
+
+build-arch: build-arch-stamp
+build-arch-stamp:  config.status
+
+	# Compile the arch part of the package
+	$(MAKE) 
+	touch $@
+
+clean: unpatch
+	dh_testdir
+	dh_testroot
+
+	# Clean up after the build process...
+
+	[ ! -f Makefile ] || $(MAKE) distclean
+	rm -rf autom4te.cache
+	rm -f aclocal.m4 configure _configs.sed
+	rm -f Makefile.in btk/Makefile.in btk/core/Makefile.in 
+	rm -f examples/Makefile.in 
+	rm -f tests/Makefile.in tests/output_test.pdb
+	rm -f btk/core/config/btk_core_config.h
+	rm -f config.sub config.guess
+
+	dh_clean 
+
+install: 
+	dh_testdir
+	dh_testroot
+	dh_clean -k -s 
+	dh_installdirs -s
+
+	# Install the arch part of the package into debian/tmp
+	$(MAKE) DESTDIR=$(CURDIR)/debian/tmp install
+
+	dh_install --sourcedir=debian/tmp
+
+binary-common:
+	dh_testdir
+	dh_testroot
+	dh_installchangelogs
+	dh_installdocs
+	dh_installexamples
+	dh_installman
+	dh_link
+	dh_strip
+	dh_compress 
+	dh_fixperms
+	dh_makeshlibs
+	dh_installdeb
+	dh_shlibdeps
+	dh_gencontrol
+	dh_md5sums
+	dh_builddeb
+
+# Build architecture dependant packages using the common target.
+binary-arch: build-arch install
+	$(MAKE) -f debian/rules DH_OPTIONS=-s binary-common
+
+binary: binary-arch
+.PHONY: build clean binary-arch binary install install-arch 


Property changes on: trunk/packages/btk-core/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/btk-core/trunk/debian/transform_structure.1
===================================================================
--- trunk/packages/btk-core/trunk/debian/transform_structure.1	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/transform_structure.1	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,22 @@
+.TH TRANSFORM_STRUCTURE_FILE  "1" "June 2007" "User Commands"
+.SH NAME
+transform_structure \- apply a transformation to a structure
+.SH DESCRIPTION
+.B transform_structure 
+.I transform_file
+\fIpdb_file\fR
+.BI [ chain_id 
+.BI [ chain_id
+.B ]]
+.PP
+Maps structure coordinates x to x' = Ux+T for the rotation U and
+translation T specified in \fItransform_file\fR.
+.SH "SEE ALSO"
+.B rmsd
+(1)
+.SH AUTHORS
+\fBtransform_structure_file\fR was written by the BTK project
+(http://projects.sf.net/btk)
+.PP
+This manual page was written for the Ubuntu project by Morten Kjeldgaard
+<mok at bioxray.dk>

Added: trunk/packages/btk-core/trunk/debian/watch
===================================================================
--- trunk/packages/btk-core/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/btk-core/trunk/debian/watch	2008-01-10 15:57:48 UTC (rev 1096)
@@ -0,0 +1,10 @@
+# This file is an input file for uscan (1) to check for upstream updates
+# and more.  See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+# Find new files on sourceforge, for debscripts >= 2.9
+http://sf.net/btk/btk_core-(.*)\.tar\.gz
+
+####




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