Split off applications in a single sub-package
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2 changed files with 90 additions and 37 deletions
29
seqan2-SIMD_vectorization_warning.patch
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29
seqan2-SIMD_vectorization_warning.patch
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From 2936cd92331f6738c13cc6f7620647d6a05a831a Mon Sep 17 00:00:00 2001
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From: marehr <marehr-github@marehr.dialup.fu-berlin.de>
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Date: Mon, 15 Jan 2018 14:31:04 +0100
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Subject: [PATCH] [FIX#2223] "No supported platform for SIMD vectorization!" on
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PPC64
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---
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include/seqan/simd/simd_base_seqan_impl.h | 8 ++++++--
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1 file changed, 6 insertions(+), 2 deletions(-)
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diff --git a/include/seqan/simd/simd_base_seqan_impl.h b/include/seqan/simd/simd_base_seqan_impl.h
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index ff224df84..006a2d683 100644
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--- a/include/seqan/simd/simd_base_seqan_impl.h
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+++ b/include/seqan/simd/simd_base_seqan_impl.h
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@@ -48,8 +48,12 @@
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#elif defined(PLATFORM_GCC) && (defined(__x86_64__) || defined(__i386__))
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/* GCC-compatible compiler, targeting x86/x86-64 */
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#include <x86intrin.h>
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-#else
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- #warning "No supported platform for SIMD vectorization!"
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+#elif defined(SEQAN_SIMD_ENABLED)
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+ #pragma message "You are trying to build with -DSEQAN_SIMD_ENABLED, which might be " \
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+ "auto-defined if AVX or SSE was enabled (e.g. -march=native, -msse4, ...), " \
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+ "but we only support x86/x86-64 architectures for SIMD vectorization! " \
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+ "You might want to use UME::SIMD (https://github.com/edanor/umesimd) combined " \
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+ "with -DSEQAN_UMESIMD_ENABLED for a different SIMD backend."
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#endif
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namespace seqan {
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98
seqan2.spec
98
seqan2.spec
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@ -6,25 +6,8 @@
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Name: seqan2
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Summary: C++ library of efficient algorithms and data structures
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Version: 2.4.0
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Release: 0.2.%{date}git%(echo %{checkout} | cut -c-6)%{?dist}
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## Seqan apps are licenses under BSD and GPLv3+ and LGPLv3+.
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#
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# BSD (3-clauses): alf, bs_tools, fiona, fx_tools, gustaf
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# insegt, mason2, ngs_roi, param_chooser, rabema, razers3
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# sak, sam2matrix, samcat, searchjoin, seqcons2, yara
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# ngs_roi, pair_align, ngs_roi.
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#
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# GPLv3+: rabema.
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#
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# LGPLv3+: dfi, insegt, micro_razers, pair_align
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# param_chooser, razers, razers3, rep_sep, sak
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# seqan_tcoffee, sgip, snp_store, splazers, stellar
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# tree_recon.
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##
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# LGPLv3 gives you permission to relicense the code under GPLv3
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# BSD (3-clauses) is compatible with GPLv3
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# We can use a collective license:
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License: GPLv3+ and BSD and LGPLv3+
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Release: 0.3.%{date}git%(echo %{checkout} | cut -c-6)%{?dist}
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License: BSD
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URL: http://www.seqan.de/
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Source0: https://github.com/seqan/seqan/archive/%{checkout}.zip#/seqan-%{checkout}.zip
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@ -37,6 +20,9 @@ Patch1: %{name}-set_config_filepath.patch
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# Set paths of plot.awk and ps2pswLinks.gawk files
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Patch2: %{name}-set_awk_installation.patch
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# https://github.com/seqan/seqan/issues/2223
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Patch3: %{name}-SIMD_vectorization_warning.patch
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BuildRequires: qt4-devel
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BuildRequires: cmake, gcc-c++
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BuildRequires: llvm-devel
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@ -55,12 +41,6 @@ BuildRequires: python2-pytest
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BuildRequires: python2-jinja2
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%endif
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Requires: gawk%{?_isa}
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# 'seqan2' is a very recent version of 'seqan'
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Obsoletes: seqan <= 0:1.4.2
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Provides: seqan = 0:%{version}-%{release}
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## Bundled files exception https://fedorahosted.org/fpc/ticket/174
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Provides: bundled(gnulib)
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@ -69,10 +49,49 @@ SeqAn (version 2.x.x) is an open source C++ library of efficient algorithms
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and data structures for the analysis of sequences with the focus on
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biological data.
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Our library applies a unique generic design that guarantees high performance,
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generality, extensibility, and integration with other libraries.
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generality, extensibility, and integration with other libraries.
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%package devel
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Summary: SeqAn (2.x.x) development files
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As such, it contains algorithms and data structures for
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* string representation and their manipluation,
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* online and indexed string search,
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* efficient I/O of bioinformatics file formats,
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* sequence alignments, and
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* many, many more.
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%package apps
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Summary: SeqAn (2.x.x) applications
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## Seqan apps are licenses under BSD and GPLv3+ and LGPLv3+.
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#
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# BSD (3-clauses): alf, bs_tools, fiona, fx_tools, gustaf
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# insegt, mason2, ngs_roi, param_chooser, rabema, razers3
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# sak, sam2matrix, samcat, searchjoin, seqcons2, yara
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# ngs_roi, pair_align, ngs_roi.
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#
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# GPLv3+: rabema.
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#
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# LGPLv3+: dfi, insegt, micro_razers, pair_align
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# param_chooser, razers, razers3, rep_sep, sak
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# seqan_tcoffee, sgip, snp_store, splazers, stellar
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# tree_recon.
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##
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# LGPLv3 gives you permission to relicense the code under GPLv3
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# BSD (3-clauses) is compatible with GPLv3
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# We can use a collective license:
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License: GPLv3+ and BSD and LGPLv3+
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Requires: gawk%{?_isa}
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# 'seqan2' is a very recent version of 'seqan'
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Obsoletes: seqan <= 0:1.4.2
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Provides: seqan = 0:%{version}-%{release}
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%description apps
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All SeqAn applications.
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%package headers
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Summary: SeqAn (2.x.x) headers only files
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# bzip2stream and zipstream libraries are distributed under zlib/libpng
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# basic/boost*.h libraries are distributed under Boost
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@ -83,8 +102,8 @@ License: GPLv3+ and BSD and MIT and LGPLv3+ and zlib and Boost
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Provides: bundled(bzip2stream)
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Provides: bundled(zipstream)
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%description devel
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Developer files for SeqAn, in the form for C header files.
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%description headers
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C headers files of SeqAn, including pkconfig and CMake configuration files.
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%package examples
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Summary: SeqAn (2.x.x) examples
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@ -125,6 +144,7 @@ Info files of SeqAn2's apps.
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%patch0 -p0
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%patch1 -p0
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%patch2 -p0
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%patch3 -p1
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## Remove spurious executable permissions
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for i in `find . -type f \( -name "*.h" -o -name "*.cpp" \)`; do
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@ -226,7 +246,7 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags}
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%endif
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%endif
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%files
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%files apps
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%license LICENSE
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%license apps/*/*-LICENSE apps/rabema/rabema-COPYING
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%doc README.rst CHANGELOG.rst
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@ -238,12 +258,7 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags}
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%{_datadir}/%{name}/pdf_plot_helper/plot.awk
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%{_datadir}/%{name}/pdf_plot_helper/ps2pswLinks.gawk
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%files doc
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%license LICENSE
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%doc README.rst CHANGELOG.rst
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%{_pkgdocdir}/
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%files devel
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%files headers
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%license include/seqan/LICENSE
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%doc README.rst CHANGELOG.rst
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%{_includedir}/%{name}/
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@ -254,7 +269,16 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags}
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%{_libexecdir}/%{name}/
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%exclude %{_libexecdir}/%{name}/examples/*/LICENSE
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%files doc
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%license LICENSE
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%doc README.rst CHANGELOG.rst
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%{_pkgdocdir}/
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%changelog
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* Tue Jan 16 2018 Antonio Trande <sagitterATfedoraproject.org> - 2.4.0-0.3.20180103git8a875d
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- Split off applications in a single sub-package
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- Devel rpm renamed seqan-headers
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* Sat Jan 13 2018 Antonio Trande <sagitterATfedoraproject.org> - 2.4.0-0.2.20180103git8a875d
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- plot.awk/ps2pswLinks.gawk installed in a private share datadir
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- plot.awk/ps2pswLinks.gawk symliked in '_bindir'
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