debian/0000755000000000000000000000000012171441213007162 5ustar debian/copyright0000644000000000000000000000564112171441213011123 0ustar This package was debianized by Julien Dutheil on Wed, 06 Mar 2013 14:34:00 +0100. It was downloaded from Upstream Author: Julien Dutheil Copyright: Copyright (C) 2013 Bio++ Development Team License: 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 2 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 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 General Public License can be found in `/usr/share/common-licenses/GPL'. The Debian packaging is (C) 2013, Julien Dutheil and is licensed under the GPL, see above. The provided software is distributed under the CeCILL license: This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. 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The complete text of the license may be found here: http://www.cecill.info/licences/Licence_CeCILL_V2-en.html debian/changelog0000644000000000000000000000054712171441213011042 0ustar libbpp-seq-omics (2.1.0-1) unstable; urgency=low * Maf to VCF tool added as a MafIterator. -- Julien Dutheil Wed, 06 Mar 2013 14:34:00 +0100 libbpp-seq-omics (2.0.3-1) unstable; urgency=low * Initial release, forking from bpp-seq. -- Julien Dutheil Tue, 06 Nov 2012 14:05:00 +0100 debian/prerm0000755000000000000000000000121712171441213010236 0ustar #! /bin/bash # Abort if any command returns an error value set -e removeGeneric() { if [ -f $1.all ] then echo "-- Remove generic include file: $1.all" rm $1.all fi for file in "$1"/* do if [ -d "$file" ] then # Recursion: removeGeneric $file fi done } case "$1" in remove|upgrade|deconfigure) # Actualize .all files removeGeneric /usr/include/Bpp ;; failed-upgrade) echo "$1" ;; *) echo "prerm called with unknown argument \`$1'" >&2 exit 1 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 debian/rules0000755000000000000000000000540512171441213010246 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # 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. # 24/01/10 Modification for use with CMake by Julien Dutheil. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 # 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 # shared library versions version=`ls src/lib*.so.* | \ awk '{if (match($$0,/[0-9]+\.[0-9]+\.[0-9]+$$/)) print substr($$0,RSTART)}'` major=`ls src/lib*.so.* | \ awk '{if (match($$0,/\.so\.[0-9]+$$/)) print substr($$0,RSTART+4)}'` configure: cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_TESTING=OFF . config.status: configure dh_testdir build: build-arch build-indep build-arch: build-stamp build-indep: build-stamp build-stamp: config.status dh_testdir # Add here commands to compile the package. $(MAKE) touch $@ clean: dh_testdir dh_testroot # Add here commands to clean up after the build process. [ ! -f Makefile ] || $(MAKE) clean; [ ! -f Makefile ] || rm Makefile; [ ! -f src/Makefile ] || rm src/Makefile; [ ! -f test/Makefile ] || rm test/Makefile; rm -f config.sub config.guess rm -f build-stamp rm -f CMakeCache.txt rm -f *.cmake rm -f src/*.cmake rm -f test/*.cmake rm -rf CMakeFiles rm -rf src/CMakeFiles rm -rf test/CMakeFiles rm -rf _CPack_Packages rm -rf Testing rm -f DartConfiguration.tcl dh_clean install: build dh_testdir dh_testroot dh_prep dh_installdirs # Add here commands to install the package into debian/tmp $(MAKE) DESTDIR=$(CURDIR)/debian/tmp install # Build architecture-independent files here. binary-indep: build install # We have nothing to do by default. # Build architecture-dependent files here. binary-arch: build install dh_testdir dh_testroot dh_installchangelogs ChangeLog dh_installdocs dh_installexamples dh_install # dh_installmenu # dh_installdebconf # dh_installlogrotate # dh_installemacsen # dh_installpam # dh_installmime # dh_installinit # dh_installcron # dh_installinfo dh_installman dh_link dh_strip dh_compress dh_fixperms # dh_perl # dh_python dh_makeshlibs dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb binary: binary-indep binary-arch .PHONY: build clean binary-indep binary-arch binary install debian/postrm0000755000000000000000000000217112171441213010435 0ustar #! /bin/bash # Abort if any command returns an error value set -e createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } case "$1" in remove) # Automatically added by dh_makeshlibs ldconfig # Actualize .all files createGeneric /usr/include/Bpp ;; purge|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear) echo $1 ;; *) echo "postrm called with unknown argument \`\$1'" >&2 exit 0 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 debian/compat0000644000000000000000000000000212171441213010360 0ustar 5 debian/postinst0000755000000000000000000000206212171441213010773 0ustar #! /bin/bash # Abort if any command returns an error value set -e createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } case "$1" in configure) # Actualize .all files createGeneric /usr/include/Bpp ;; abort-upgrade|abort-remove|abort-deconfigure) echo "$1" ;; *) echo "postinst called with unknown argument \`\$1'" >&2 exit 0 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 debian/libbpp-seq-omics-dev.install0000644000000000000000000000011612171441213014472 0ustar debian/tmp/usr/include/* debian/tmp/usr/lib/lib*.a debian/tmp/usr/lib/lib*.so debian/control0000644000000000000000000000142712171441213010571 0ustar Source: libbpp-seq-omics Section: libs Priority: optional Maintainer: Loic Dachary Uploaders: Julien Dutheil Build-Depends: debhelper (>= 5), cmake (>= 2.6), libbpp-seq-dev (>= 2.1.0) Standards-Version: 3.9.4 Package: libbpp-seq-omics-dev Section: libdevel Architecture: any Depends: libbpp-seq-omics1 (= ${binary:Version}), ${misc:Depends}, libbpp-seq-dev (>= 2.1.0) Description: Bio++ Sequence library: genomics components. Contains the Bio++ sequence classes dedicated to genomics. Package: libbpp-seq-omics1 Section: libs Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libbpp-seq9 (>= 2.1.0) Description: Bio++ Sequence library: genomics components. Contains the Bio++ sequence classes dedicated to genomics. debian/source/0000755000000000000000000000000012171441213010462 5ustar debian/source/format0000644000000000000000000000001412171441213011670 0ustar 3.0 (quilt) debian/libbpp-seq-omics1.install0000644000000000000000000000003512171441213013777 0ustar debian/tmp/usr/lib/lib*.so.*