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 <[email protected]> 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 <[email protected]> + * XS-DM-Upload-Allowed: Yes + * Vcs-Browser, Vcs-Svn + + -- Morten Kjeldgaard <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Morten Kjeldgaard <[email protected]> +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 <[email protected]>, + Chris Saunders <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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_@[email protected] 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_@[email protected] libbtk_core.a + + install-data-hook: +- if [ -e $(includedir)/btk/core ]; \ +- then rm -f $(includedir)/btk/core; fi +- cd $(includedir)/btk && @LN_S@ @PACKAGE@_@VERSION@ core ++ if [ -e $(DESTDIR)/$(includedir)/btk/core ]; \ ++ then rm -f $(DESTDIR)/$(includedir)/btk/core; fi ++ cd $(DESTDIR)/$(includedir)/btk && @LN_S@ @PACKAGE@_@VERSION@ core + + uninstall-hook: +- cd $(pkglibdir) && rm -f libbtk_core.a +- cd $(includedir)/btk && rm -fr core @PACKAGE@_@VERSION@ ++ cd $(DESTDIR)/$(pkglibdir) && rm -f libbtk_core.a ++ cd $(DESTDIR)/$(includedir)/btk && rm -fr core @PACKAGE@_@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 +<[email protected]> 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 +<[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/btk-core.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
