Name: lagan Version: 2.0 Release: 42%{?dist} Summary: Local, global, and multiple alignment of DNA sequences License: GPLv2 URL: http://lagan.stanford.edu Source0: http://lagan.stanford.edu/lagan_web/lagan20.tar.gz Patch0: lagan20-chris.patch Patch1: lagan20-gcc10.patch Patch2: lagan-c99.patch BuildRequires: perl-generators BuildRequires: gcc-c++ BuildRequires: make %description LAGAN toolkit is a set of tools for local, global, and multiple alignment of DNA sequences. Please visit http://lagan.stanford.edu for publications describing LAGAN and its components. The 4 main parts of LAGAN are: 1. CHAOS local alignment tool 2. LAGAN pairwise global alignment tool 3. MLAGAN multiple global alignment tool. 4. Shuffle-LAGAN pairwise global alignment %prep %setup -q -n lagan20 %patch -P0 -p1 -b .chris %patch -P1 -p1 -b .gcc10 %patch -P2 -p1 sed -i 's/^CC .*$/CC = gcc $(RPM_OPT_FLAGS)/; s/^CPP .*$/CPP = g++ $(RPM_OPT_FLAGS)/' Makefile sed -i 's|getenv ("LAGAN_DIR")|"%_libdir/lagan"|g' src/*.c src/utils/*.c sed -i 's|getenv ("LAGAN_DIR")|"%_libdir/lagan"|g' src/utils/*.cpp sed -i 's|$ENV{LAGAN_DIR}|"%_libdir/lagan"|g' *.pl src/*.pl utils/*.pl src/utils/*.pl sed -i 's|$LAGAN_DIR|%_libdir/lagan|g' Readmes/README.shuffle src/*.c sed -i 's/getline/GetLine/g' src/anchors.c sed -i 's/^inline /inline __attribute__ ((always_inline)) /' src/fchaos.c sed -i '//a#include ' src/filebuffer.c sed -i '//a#include ' src/utils/scorecontigs.c sed -i '//a#include ' src/utils/overlay.c sed -i '//a#include ' src/utils/cstat.c sed -i 's/^int indeces/extern int indeces/' src/thrtrie.h sed -i '/^int nnodes=0;/aint indeces[256];' src/thrtrie.c rm prolagan chmod -x src/glocal/* %build make %{?_smp_mflags} CFLAGS="$RPM_OPT_FLAGS" CXXFLAGS="$RPM_OPT_FLAGS" %install rm -rf $RPM_BUILD_ROOT mkdir -p $RPM_BUILD_ROOT/%_bindir $RPM_BUILD_ROOT/%_libdir/lagan/utils install -m755 chaos ${RPM_BUILD_ROOT}%{_bindir} install -m755 mlagan ${RPM_BUILD_ROOT}%{_bindir} install -m755 prolagan ${RPM_BUILD_ROOT}%{_bindir} install -m755 lagan.pl ${RPM_BUILD_ROOT}%{_bindir}/lagan install -m755 slagan.pl ${RPM_BUILD_ROOT}%{_bindir}/slagan for f in anal_gloc.pl anchors glocal order rechaos.pl \ supermap.pl xmfa2mfa.pl; do install -m755 $f $RPM_BUILD_ROOT/%_libdir/lagan done for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot \ draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue \ mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl \ mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay; do install -m755 utils/$f $RPM_BUILD_ROOT/%_libdir/lagan/utils done install -m644 *.txt *.score $RPM_BUILD_ROOT/%_libdir/lagan rm -f Readmes/*.chris %files %doc Readmes/* sample.* %_bindir/chaos %_bindir/lagan %_bindir/mlagan %_bindir/slagan %_bindir/prolagan %_libdir/lagan/ %changelog * Thu Jul 18 2024 Fedora Release Engineering - 2.0-42 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild * Thu Jan 25 2024 Fedora Release Engineering - 2.0-41 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Sun Jan 21 2024 Fedora Release Engineering - 2.0-40 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Thu Jul 20 2023 Fedora Release Engineering - 2.0-39 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Thu Jan 19 2023 Fedora Release Engineering - 2.0-38 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Fri Jan 13 2023 Florian Weimer - 2.0-37 - C99 compatibility fixes (#2160661) * Thu Jul 21 2022 Fedora Release Engineering - 2.0-36 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Thu Jan 20 2022 Fedora Release Engineering - 2.0-35 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Thu Jul 22 2021 Fedora Release Engineering - 2.0-34 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Tue Jan 26 2021 Fedora Release Engineering - 2.0-33 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Tue Jul 28 2020 Fedora Release Engineering - 2.0-32 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Fri Feb 21 2020 Christian Iseli - 2.0-31 - Fix FTBFS due to variable multiple definition issues (bz 1799571) * Wed Jan 29 2020 Fedora Release Engineering - 2.0-30 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Tue Dec 17 2019 Jeff Law - 2.0-29 - Fix another inline vs static inline issue for gcc-10/LTO * Sat Dec 14 2019 Jeff Law - 2.0-28 - Fix inline vs static inline issue for gcc-10 * Tue Sep 10 2019 Christian Iseli - 2.0-27 - Fix FTBFS due to inlining issue (bz 1729180) * Thu Jul 25 2019 Fedora Release Engineering - 2.0-26 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Fri Feb 01 2019 Fedora Release Engineering - 2.0-25 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Mon Jul 23 2018 Christian Iseli - 2.0-24 - Fix FTBFS due to missing BuildRequires gcc-c++ (bz 1604535) - Fix typo shown by rpmlint * Fri Jul 13 2018 Fedora Release Engineering - 2.0-24 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Wed Feb 07 2018 Fedora Release Engineering - 2.0-23 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Thu Aug 03 2017 Fedora Release Engineering - 2.0-22 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Wed Jul 26 2017 Fedora Release Engineering - 2.0-21 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Fri Feb 10 2017 Fedora Release Engineering - 2.0-20 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Mon Feb 29 2016 Christian Iseli - 2.0-19 - Fix FTBFS bugzilla 1307708 * Thu Feb 04 2016 Fedora Release Engineering - 2.0-18 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Wed Jun 17 2015 Fedora Release Engineering - 2.0-17 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Sat May 02 2015 Kalev Lember - 2.0-16 - Rebuilt for GCC 5 C++11 ABI change * Sun Aug 17 2014 Fedora Release Engineering - 2.0-15 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Sat Jun 07 2014 Fedora Release Engineering - 2.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Sat Aug 03 2013 Fedora Release Engineering - 2.0-13 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Wed Jul 17 2013 Petr Pisar - 2.0-12 - Perl 5.18 rebuild * Thu Feb 14 2013 Fedora Release Engineering - 2.0-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild * Thu Jul 19 2012 Fedora Release Engineering - 2.0-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild * Tue Feb 28 2012 Fedora Release Engineering - 2.0-9 - Rebuilt for c++ ABI breakage * Fri Jan 13 2012 Fedora Release Engineering - 2.0-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild * Mon Feb 07 2011 Fedora Release Engineering - 2.0-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild * Fri Jul 24 2009 Fedora Release Engineering - 2.0-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild * Fri Jun 5 2009 Christian Iseli - 2.0-5 - Add fix for getline() conflicting with stdio.h definition in new glibc * Wed Feb 25 2009 Fedora Release Engineering - 2.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild * Mon Feb 23 2009 Christian Iseli - 2.0-3 - Rebuild for F-11 * Sun Jan 27 2008 Christian Iseli - 2.0-2 - Update patch to fix gcc-4.3 compilation issues. * Tue Sep 18 2007 Christian Iseli - 2.0-1 - New upstream release. * Wed Aug 22 2007 Christian Iseli - 1.21-4 - Fix License tag. * Tue Sep 05 2006 Christian Iseli - 1.21-3 - Rebuild for FC 6. * Wed Feb 15 2006 Christian Iseli - 1.21-2 - Rebuild for FE 5. * Mon Jan 30 2006 Christian Iseli - 1.21-1 - Use _libdir instead of _libexecdir and kill all LAGAN_DIR refs. * Thu Nov 17 2005 Christian Iseli - 1.21-0 - Create spec file.