.gitignore

@@ -0,0 +1,4 @@
+/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

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

seqan-docpath.patch

@@ -0,0 +1,11 @@
+--- 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

@@ -0,0 +1,23 @@
+--- 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

@@ -0,0 +1,23 @@
+--- 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

@@ -0,0 +1,251 @@
+Name:      seqan
+Summary:   Open source C++ library of efficient algorithms and data structures
+Version:   1.4.2
+Release:   26%{?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: 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: python-nose
+BuildRequires: pytest
+BuildRequires: python-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 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

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