[med-svn] [btk-core] 13/15: Re-add debian/ dir
Andreas Tille
tille at debian.org
Sun Dec 24 22:56:56 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository btk-core.
commit 9272a76adf5ecac6e5fee787e4129a3230984245
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 24 23:39:10 2017 +0100
Re-add debian/ dir
---
debian/changelog | 24 +++++++
debian/compat | 1 +
debian/control | 24 +++++++
debian/copyright | 29 ++++++++
debian/docs | 3 +
debian/libbtk-core-dev.examples | 3 +
debian/libbtk-core-dev.install | 2 +
debian/patches/00list | 2 +
debian/patches/100-Makefile.am.dpatch | 16 +++++
debian/patches/100-btk_core_Makefile.am.dpatch | 31 +++++++++
debian/rmsd.1 | 53 +++++++++++++++
debian/rules | 94 ++++++++++++++++++++++++++
debian/transform_structure.1 | 22 ++++++
debian/watch | 3 +
14 files changed, 307 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..87760c4
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,24 @@
+btk-core (0.8.1-1) UNRELEASED; urgency=low
+
+ [ Morten Kjeldgaard ]
+ * Modified for upload to Debian (Closes #459753)
+ * Use standards versions 3.7.3
+
+ [ Andreas Tille ]
+ * Maintainer: Debian-Med Packaging Team
+ Uploaders: Morten Kjeldgaard <mok at bioxray.dk>
+ * XS-DM-Upload-Allowed: Yes
+ * Vcs-Browser, Vcs-Svn
+
+ -- 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
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..9c79a8c
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: btk-core
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Morten Kjeldgaard <mok at bioxray.dk>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 10),
+ automake,
+ libboost-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/btk-core/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/btk-core/trunk/
+Homepage: http://btk.sourceforge.net/
+
+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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..339a8b6
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,29 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Tim Robertson <kid50 at users.sourceforge.net>,
+ Chris Saunders <ctsa at users.sourceforge.net>
+Source: http://sourceforge.net/projects/btk/
+
+Files: btk/*, examples/*, tests/*
+Copyright: 2006 Tim Robertson, Chris Saunders, Alex Morozov, Eric Alm
+ & Jeff Gray
+License: LGPL-2.1+
+ 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
+
+Files: debian/*
+Copyright: (C) 2007, Morten Kjeldgaard <mok at bioxray.dk>
+License: LGPL-2.1+
+
+X-Comment: On Debian systems, the complete text of the GNU Lesser General
+ Public License can be found in `/usr/share/common-licenses/LGPL-2.1'.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..2e33b51
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+NEWS
+README
+HACKING
diff --git a/debian/libbtk-core-dev.examples b/debian/libbtk-core-dev.examples
new file mode 100644
index 0000000..2131d39
--- /dev/null
+++ b/debian/libbtk-core-dev.examples
@@ -0,0 +1,3 @@
+examples/*.cpp
+debian/rmsd.1
+debian/transform_structure.1
diff --git a/debian/libbtk-core-dev.install b/debian/libbtk-core-dev.install
new file mode 100644
index 0000000..451eacc
--- /dev/null
+++ b/debian/libbtk-core-dev.install
@@ -0,0 +1,2 @@
+usr/include/btk
+usr/lib
diff --git a/debian/patches/00list b/debian/patches/00list
new file mode 100644
index 0000000..a4ab5ee
--- /dev/null
+++ b/debian/patches/00list
@@ -0,0 +1,2 @@
+100-Makefile.am.dpatch
+100-btk_core_Makefile.am.dpatch
diff --git a/debian/patches/100-Makefile.am.dpatch b/debian/patches/100-Makefile.am.dpatch
new file mode 100644
index 0000000..30782f6
--- /dev/null
+++ b/debian/patches/100-Makefile.am.dpatch
@@ -0,0 +1,16 @@
+Author: Morten Kjeldgaard <mok at bioxray.dk>
+Description: Remove the uninstall-hook in top level Makefile.am
+
+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
diff --git a/debian/patches/100-btk_core_Makefile.am.dpatch b/debian/patches/100-btk_core_Makefile.am.dpatch
new file mode 100644
index 0000000..dc284e6
--- /dev/null
+++ b/debian/patches/100-btk_core_Makefile.am.dpatch
@@ -0,0 +1,31 @@
+Author: Morten Kjeldgaard <mok at bioxray.dk>
+Description: Use $DESTDIR in this Makefile.am
+
+--- 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@
diff --git a/debian/rmsd.1 b/debian/rmsd.1
new file mode 100644
index 0000000..3c45562
--- /dev/null
+++ b/debian/rmsd.1
@@ -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>
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..d15a97e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,94 @@
+#!/usr/bin/make -f
+
+# 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 ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+CFLAGS = -Wall -g
+
+ifneq (,$(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
diff --git a/debian/transform_structure.1 b/debian/transform_structure.1
new file mode 100644
index 0000000..03cb81a
--- /dev/null
+++ b/debian/transform_structure.1
@@ -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>
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..85e4705
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+http://sf.net/btk/btk_core-(.*)\.tar\.gz
--
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