%if 0%{?epel} < 7 %{!?__global_ldflags: %global __global_ldflags -Wl,-z,relro} %endif Name: wise2 Version: 2.4.1 Release: 16%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for ## the HMMer2 libraries and models directory which are GPLv2+ ## see LICENSE files for details. License: BSD and GPLv2+ URL: http://www.ebi.ac.uk/~birney/%{name}/ Source0: http://www.ebi.ac.uk/~birney/%{name}/wise%{version}.tar.gz ## Patches from Debian package. Thanks to Philipp Benner Patch0: %{name}-build.patch Patch1: %{name}-isnumber.patch Patch2: %{name}-glib2.patch Patch3: %{name}-getline.patch Patch4: %{name}-ld--as-needed.patch Patch5: %{name}-mayhem.patch Patch6: %{name}-c99.patch BuildRequires: make BuildRequires: glib2-devel, gcc, perl BuildRequires: strace BuildRequires: pkgconfig %description Wise2 is a package focused on comparisons of bio-polymers, commonly DNA sequence and protein sequence. A strength of Wise2 is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of gene structure with homology based alignment. %package doc Summary: Wise2 documentation BuildArch: noarch %description doc Wise2, Wise2api and Dynamite documentation files. %package examples Summary: Wise2 examples Requires: %{name}%{?_isa} = %{version}-%{release} %description examples Here are some examples that you might want to try out. The Wise2 executables of course should be installed before. %prep %setup -q -n wise%{version} %patch0 -p1 %patch1 -p1 %patch2 -p1 %patch3 -p1 %patch4 -p1 %patch6 -p1 # Remove spurious-executable-perm chmod a-x src/external/mott/mott_api.c chmod a-x src/external/mott/mott_api.h chmod a-x src/external/mott/gaplib.c chmod a-x src/external/mott/gapstat.h ## fix interpreter in examples sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' docs/gettex.pl ## fix perms chmod -x test_data/rrm.HMM ## pull out licenses for i in base dynlibsrc dyc do cp src/$i/LICENSE LICENSE.$i done cp src/models/GNULICENSE LICENSE.GPL %build ## removed "{?_smp_mflags}", does not support parallel build export LDFLAGS="%{__global_ldflags}" make -C src CC=gcc \ CFLAGS=" -c $RPM_OPT_FLAGS -pthread -D_GNU_SOURCE %(pkg-config --cflags glib-2.0) -D_POSIX_C_SOURCE=200112L" all %install pushd src/bin mkdir -p $RPM_BUILD_ROOT%{_bindir} for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb do install -pm 755 $i $RPM_BUILD_ROOT%{_bindir} done popd # install architecture-independent data and config files mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2 pushd wisecfg install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2 popd # install architecture-independent files to run example tests mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2/examples pushd test_data install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2/examples popd # install scripts to automatically set the WISECONFIGDIR environment variable mkdir -p $RPM_BUILD_ROOT%{_sysconfdir}/profile.d echo "export WISECONFIGDIR=%{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.sh echo "setenv WISECONFIGDIR %{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.csh %check export WISECONFIGDIR=$PWD/wisecfg make -C src test %files %doc README %license LICENSE LICENSE.base LICENSE.dynlibsrc LICENSE.dyc LICENSE.GPL %{_bindir}/genewisedb %{_bindir}/estwisedb %{_bindir}/genewise %{_bindir}/estwise %{_bindir}/scanwise %{_bindir}/promoterwise %{_bindir}/pswdb %{_bindir}/dba %{_bindir}/psw %{_bindir}/scanwise_server %{_bindir}/dnal %{_datadir}/wise2/ %config(noreplace) %{_sysconfdir}/profile.d/* %files doc %license LICENSE %doc docs %files examples %doc test_data/README %{_datadir}/wise2/examples/ %changelog * Fri Dec 23 2022 Peter Fordham - 2.4.1-16 - Fix build for C99 compliance by adding missing headers. * Sat Jul 23 2022 Fedora Release Engineering - 2.4.1-15 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Sat Jan 22 2022 Fedora Release Engineering - 2.4.1-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Fri Jul 23 2021 Fedora Release Engineering - 2.4.1-13 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Wed Jan 27 2021 Fedora Release Engineering - 2.4.1-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Wed Jul 29 2020 Fedora Release Engineering - 2.4.1-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Fri Jan 31 2020 Fedora Release Engineering - 2.4.1-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Sat Jul 27 2019 Fedora Release Engineering - 2.4.1-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Sun Feb 03 2019 Fedora Release Engineering - 2.4.1-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Sat Jul 14 2018 Fedora Release Engineering - 2.4.1-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Thu Feb 22 2018 Antonio Trande - 2.4.1-6 - Add gcc perl BR * Fri Feb 09 2018 Fedora Release Engineering - 2.4.1-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Thu Aug 03 2017 Fedora Release Engineering - 2.4.1-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Thu Jul 27 2017 Fedora Release Engineering - 2.4.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Sat Feb 11 2017 Fedora Release Engineering - 2.4.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Tue May 05 2015 Antonio Trande - 2.4.1-1 - Update to 2.4.1 - Fix compiler flags * Sun Aug 04 2013 Fedora Release Engineering - 2.2.0-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Fri Feb 15 2013 Fedora Release Engineering - 2.2.0-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild * Sun Jul 22 2012 Fedora Release Engineering - 2.2.0-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild * Sat Jan 14 2012 Fedora Release Engineering - 2.2.0-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild * Mon Feb 07 2011 Fedora Release Engineering - 2.2.0-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild * Mon Jul 27 2009 Fedora Release Engineering - 2.2.0-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild * Thu Jul 16 2009 Alex Lancaster - 2.2.0-6 - Add -D_POSIX_C_SOURCE=200112L to CFLAGS as a workaround to fix FTBFS (#511627) * Wed Feb 25 2009 Fedora Release Engineering - 2.2.0-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild * Sat Feb 9 2008 Alex Lancaster - 2.2.0-4 - rebuilt for GCC 4.3 as requested by Fedora Release Engineering * Thu Aug 16 2007 Alex Lancaster 2.2.0-3 - Clarify license as BSD and GPLv2+ * Thu Apr 12 2007 Alex Lancaster 2.2.0-2 - Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius. * Wed Apr 11 2007 Alex Lancaster 2.2.0-1 - Initial Fedora package.