No longer needed in Fedora; deprecated by seqan3

Signed-off-by: Fedora Release Engineering <releng@fedoraproject.org>

.gitignore

@@ -1,4 +0,0 @@
-/seqan-src-1.4.1.tar.gz
-/seqan-src-1.4.2.tar.gz
-/seqan-seqan-v2.0.0-rc1.tar.gz
-/seqan-seqan-v2.0.0.tar.gz

dead.package

@@ -0,0 +1 @@
+No longer needed in Fedora; deprecated by seqan3

seqan-docpath.patch

@@ -1,11 +0,0 @@
---- util/cmake/SeqAnBuildSystem-orig.cmake	2013-11-20 10:46:58.000000000 +0100
-+++ util/cmake/SeqAnBuildSystem.cmake	2014-06-14 22:28:18.112533516 +0200
-@@ -308,6 +308,7 @@
-     else ()
-         set (SEQAN_PREFIX_SHARE "share/${APP_NAME}")
-         set (SEQAN_PREFIX_SHARE_DOC "share/doc/${APP_NAME}")
-+        set (SEQAN_PREFIX_SHARE_DOC "share/doc/seqan/${APP_NAME}")
-     endif ()
- endmacro (seqan_setup_install_vars)
- 
-

seqan-exclude_bstools_test.patch

@@ -1,23 +0,0 @@
---- extras/apps/bs_tools/CMakeLists.orig.txt	2014-10-13 15:03:56.000000000 +0200
-+++ extras/apps/bs_tools/CMakeLists.txt	2014-12-02 11:38:23.759795760 +0100
-@@ -106,7 +106,7 @@
- # ----------------------------------------------------------------------------
- 
- # (weese:) temporarily disabled app test
--seqan_add_app_test (bs_tools)
-+# seqan_add_app_test (bs_tools)
- 
- # ----------------------------------------------------------------------------
- # CPack Install
---- core/apps/samcat/CMakeLists.txt	2015-05-15 16:50:20.223867704 +0200
-+++ core/apps/samcat/CMakeLists.orig.txt	2014-10-13 15:03:56.000000000 +0200
-@@ -63,7 +63,7 @@
- # App Test
- # ----------------------------------------------------------------------------
- 
--seqan_add_app_test (samcat)
-+#seqan_add_app_test (samcat)
- 
- # ----------------------------------------------------------------------------
- # Setup Common Tool Description for Generic Workflow Nodes
-

seqan-exclude_splazers_fiona_tests.patch

@@ -1,23 +0,0 @@
---- core/apps/splazers/CMakeLists.orig.txt	2014-10-13 15:03:56.000000000 +0200
-+++ core/apps/splazers/CMakeLists.txt	2014-11-25 10:41:12.804941092 +0100
-@@ -71,7 +71,7 @@
- # App Test
- # ----------------------------------------------------------------------------
- 
--seqan_add_app_test (splazers)
-+# seqan_add_app_test (splazers)
- 
- # ----------------------------------------------------------------------------
- # CPack Install
---- core/apps/fiona/CMakeLists.orig.txt	2014-10-13 15:03:56.000000000 +0200
-+++ core/apps/fiona/CMakeLists.txt	2014-11-25 10:45:11.870330056 +0100
-@@ -79,7 +79,7 @@
- # App Test
- # ----------------------------------------------------------------------------
- 
--seqan_add_app_test (fiona)
-+# seqan_add_app_test (fiona)
- 
- # ----------------------------------------------------------------------------
- # Setup Common Tool Description for Generic Workflow Nodes
-

seqan.spec

@@ -1,286 +0,0 @@
-Name:      seqan
-Summary:   Open source C++ library of efficient algorithms and data structures
-Version:   1.4.2
-Release:   37%{?dist}
-License:   BSD and GPLv3+ and LGPLv3+
-URL:       http://www.seqan.de/
-Source0:   http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz
-
-## This patch sets a seqan directory for documentation files
-Patch0: %{name}-docpath.patch
-
-## These patches exclude tests of splazers, fiona, bs_tools
-## They fail beacause unknown reasons
-Patch1: %{name}-exclude_splazers_fiona_tests.patch
-Patch2: %{name}-exclude_bstools_test.patch
-
-BuildRequires: gcc, gcc-c++
-BuildRequires: qt4-devel >= 4.7
-BuildRequires: cmake >= 2.8
-BuildRequires: llvm-devel
-BuildRequires: bzip2-devel
-BuildRequires: zlib-devel
-BuildRequires: boost-devel
-BuildRequires: coin-or-lemon-devel
-BuildRequires: libstdc++-static
-BuildRequires: java-1.8.0-openjdk-devel
-## Test
-BuildRequires: python2-devel
-BuildRequires: python2-nose
-BuildRequires: python2-pytest
-BuildRequires: python2-jinja2
-
-Requires: gawk
-
-## Bundled files exception https://fedorahosted.org/fpc/ticket/174
-Provides: bundled(gnulib)
-
-%description
-SeqAn is an open source C++ library of efficient algorithms and data structures 
-for the analysis of sequences with the focus on biological data. 
-Our library applies a unique generic design that guarantees high performance, 
-generality, extensibility, and integration with other libraries. 
-
-%package devel
-Summary: SeqAn development files
-
-%description devel
-Developer files for SeqAn, in the form for C header files.
-
-%package doc
-Summary: SeqAn documentation
-BuildArch: noarch
-
-%description doc
-Info files of SeqAn's apps.
-
-%prep
-%setup -q -n seqan-%{version}
-%patch0 -p0
-%patch1 -p0
-
-%ifarch %{arm} aarch64 %{power64} s390x
-%patch2 -p0
-%endif
-
-## Remove spurious executable permissions
-for i in `find . -perm /111 -type f \( -name "*.h" -o -name "*.cpp" \)`; do
-chmod a-x $i
-done
-
-## Renamed each single license file 
-cp -p extras/apps/rep_sep/LICENSE LGPLv3+.txt
-cp -p core/apps/rabema/LICENSE GPLv3+.txt
-cp -p LICENSE BSD.txt 
-
-## Make install needs this README file
-cp -p extras/apps/seqan_flexbar/INFO extras/apps/seqan_flexbar/README
-
-%build
-mkdir -p build/Release && pushd build/Release
-##This error comes out on >=F22
-##cc1plus: out of memory
-%ifarch %{arm} || ( 0%{?fedora} >= 22 )
-SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g')
-SEQAN_OPT_FLAGS="$SEQAN_OPT_FLAGS -fPIC -Wl,-z,now"
-%else
-SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS -fPIC -Wl,-z,now"
-%endif
-export CXXFLAGS="$SEQAN_OPT_FLAGS"
-export LDFLAGS="$RPM_LD_FLAGS -fPIC -Wl,-z,now"
-cmake \
- -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS" \
- -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \
- -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \
- -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \
- -DBUILD_SHARED_LIBS:BOOL=OFF \
- -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \
- -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \
- -DCMAKE_BUILD_TYPE:STRING=Release -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS \
- -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_APP_VERSION:STRING=%{version} \
- -DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH="-L%{_libdir} -lz" \
- -DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH="-L%{_libdir} -lbz2" \
- -DLEMON_INCLUDE_DIR:PATH=%{_includedir} -DLEMON_LIBRARY:FILEPATH="-L%{_libdir} -lemon" \
- -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python2} \
- -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE ../..
-
-##Compiler fails with parallel make
-make all
-
-%install
-%make_install -C build/Release INSTALL="install -p"
-
-## Put header files in ad-hoc include directory  
-mkdir -p %{buildroot}%{_includedir}/seqan
-cp -pr extras/include/seqan/* %{buildroot}%{_includedir}/seqan
-cp -pr core/include/seqan/* %{buildroot}%{_includedir}/seqan
-
-mkdir -p seqandoc
-cp -pr %{buildroot}%{_docdir}/seqan/* seqandoc
-rm -rf %{buildroot}%{_docdir}/seqan
-rm -f seqandoc/*.txt
-
-## Rename 'join' binary file; it conflicts with the one owned by 'coreutils' package
-mv %{buildroot}%{_bindir}/join %{buildroot}%{_bindir}/searchjoin
-
-## Fix executable permissions
-for i in `find %{buildroot}%{_bindir} -perm /644 -type f \( -name "*.sh" \)`; do
-chmod a+x $i
-done
-
-%check
-pushd build/Release
-# Skip 10 - app_test_samcat, 16 - app_test_bs_tools, 20 - app_test_ngs_roi
-%ifarch %{arm} aarch64 %{power64} s390x
-ctest -I 1,9 --force-new-ctest-process -VV -j1
-%else
-ctest --force-new-ctest-process -VV %{?_smp_mflags}
-%endif
-
-%files
-%license BSD.txt GPLv3+.txt LGPLv3+.txt
-%doc README.rst
-%{_bindir}/*
-
-%files doc
-%license BSD.txt GPLv3+.txt LGPLv3+.txt
-%doc seqandoc
-
-%files devel
-%license BSD.txt GPLv3+.txt LGPLv3+.txt
-%doc README.rst
-%{_includedir}/seqan/
-
-%changelog
-* Sat Jul 14 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-37
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
-
-* Wed Mar 07 2018 Adam Williamson <awilliam@redhat.com> - 1.4.2-36
-- Rebuild to fix GCC 8 mis-compilation
-  See https://da.gd/YJVwk ("GCC 8 ABI change on x86_64")
-
-* Thu Feb 22 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.4.2-35
-- Add gcc-c++ BR
-
-* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-34
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
-
-* Thu Aug 03 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-33
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
-
-* Sun Jul 30 2017 Florian Weimer <fweimer@redhat.com> - 1.4.2-32
-- Rebuild with binutils fix for ppc64le (#1475636)
-
-* Thu Jul 27 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-31
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
-
-* Tue Jul 04 2017 Jonathan Wakely <jwakely@redhat.com> - 1.4.2-30
-- Rebuilt for Boost 1.64
-
-* Mon May 15 2017 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.4.2-29
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild
-
-* Sat Feb 11 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-28
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
-
-* Fri Jan 27 2017 Jonathan Wakely <jwakely@redhat.com> - 1.4.2-27
-- Rebuilt for Boost 1.63
-
-* Sat Nov 12 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-26
-- Skip tests on s390 and ppc
-
-* Sat Nov 12 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-25
-- Skip failed tests
-
-* Sat Feb 20 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-24
-- Fixed compiler/linker flags
-
-* Thu Feb 04 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-23
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
-
-* Fri Jan 15 2016 Jonathan Wakely <jwakely@redhat.com> - 1.4.2-22
-- Rebuilt for Boost 1.60
-
-* Wed Oct 21 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-21
-- Actived hardened build
-
-* Tue Oct 13 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-20
-- Rebuilt for cmake 3.4.0
-- Used %%license
-
-* Thu Aug 27 2015 Jonathan Wakely <jwakely@redhat.com> - 1.4.2-19
-- Rebuilt for Boost 1.59
-
-* Wed Jul 29 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.4.2-18
-- Rebuilt for https://fedoraproject.org/wiki/Changes/F23Boost159
-
-* Sat Jul 18 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-17
-- Parallel make always disabled
-
-* Sat Jul 18 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-16
-- Rebuild for Boost upgrade to 1.58.0
-
-* Fri Jun 19 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.4.2-15
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
-
-* Fri May 15 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-14
-- Reduce optimization to -O0 (cc1plus error persists)
-
-* Fri May 15 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-13
-- SPEC cleanups
-
-* Fri May 15 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-12
-- Removed -pipe flag because of cc1plus error on ARMs
-
-* Thu May 14 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-11
-- Set job=1 to Make on ARMs aarch64 ppc64 ppc64le
-
-* Thu May 14 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-10
-- Downgrading to 1.4.2
-- Excluded s390 s390x arches
-- Excluded bstools_test on ARMs aarch64 ppc64 ppc64le
-
-* Mon Jan 26 2015 Petr Machata <pmachata@redhat.com> - 1.4.2-9
-- Rebuild for boost 1.57.0
-
-* Tue Dec 02 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-8
-- Excluded bs_tools test on ARM
-
-* Mon Dec 01 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-7
-- Parallel tests not performed on ARM
-
-* Mon Dec 01 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-6
-- DBUILD_SHARED_LIBS boolean disabled
-- Test enabled
-
-* Tue Nov 25 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-5
-- Parallel make excluded on ARM arch
-
-* Tue Nov 25 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-4
-- Tests disabled temporarily
-
-* Sat Nov 22 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-3
-- Packaged private libraries
-- Performed tests
-- Splazers and fiona tests excluded
-
-* Sat Nov 22 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-2
-- Parallel make excluded on ARM arch
-
-* Fri Nov 21 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-1
-- Update to 1.4.2
-- Fixed cmake compiler flags
-- Fixed declaration of multiple license
-- A doc sub-package is now built
-
-* Mon Aug 18 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.4.1-3
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
-
-* Sat Jun 14 2014 Antonio Trande <sagitterATfedoraproject.org> 1.4.1-2
-- Added 'Provides:bundled(gnulib)'
-- Changed find command for executable permissions fixing
-- Use %%make_install 
-- Fixed wrong-file-end-of-line-encoding warnings
- 
-* Wed Jun 11 2014 Antonio Trande <sagitterATfedoraproject.org> 1.4.1-1
-- First package

sources

@@ -1 +0,0 @@
-e7d2c6cf6474b5186c27ec31bd32738a  seqan-src-1.4.2.tar.gz