[seqan] New package (bz#1105730).

[Antonio Trande]

commit 0ca319ba9d28ad3afd35583fc3f389d2d329aa99
Author: sagitter <anto.trande at gmail.com>
Date:   Fri Jun 20 17:17:38 2014 +0200

    New package (bz#1105730).

 .gitignore          |    1 +
 seqan-docpath.patch |   11 +++++++
 seqan.spec          |   84 +++++++++++++++++++++++++++++++++++++++++++++++++++
 sources             |    1 +
 4 files changed, 97 insertions(+), 0 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index e69de29..f17a468 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/seqan-src-1.4.1.tar.gz
diff --git a/seqan-docpath.patch b/seqan-docpath.patch
new file mode 100644
index 0000000..c100b95
--- /dev/null
+++ b/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
+@@ -297,6 +297,7 @@
+     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/${APP_NAME}")
+     endif ()
+ endmacro (seqan_setup_install_vars)
+ 
+
diff --git a/seqan.spec b/seqan.spec
new file mode 100644
index 0000000..3cbea56
--- /dev/null
+++ b/seqan.spec
@@ -0,0 +1,84 @@
+Name:      seqan
+Summary:   Open source C++ library of efficient algorithms and data structures
+Version:   1.4.1
+Release:   2%{?dist}
+License:   BSD
+URL:       http://www.seqan.de/
+Source0:   http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz
+
+## This patch sets a seqan directory for documentation files
+Patch0:    %{name}-docpath.patch
+
+BuildRequires: qt4-devel >= 4.7
+BuildRequires: cmake >= 2.8 
+BuildRequires: llvm-devel, bzip2-devel, zlib-devel, boost-devel
+BuildRequires: coin-or-lemon-devel, openmpi-devel
+BuildRequires: python2-devel
+BuildRequires: java-1.7.0-openjdk-devel
+
+## Bundled files exception https://fedorahosted.org/fpc/ticket/174
+Provides: bundled(gnulib)
+
+%description
+SeqAn is an open source C++ library of efficient algorithms and data structures 
+for the analysis of sequences with the focus on biological data. 
+Our library applies a unique generic design that guarantees high performance, 
+generality, extensibility, and integration with other libraries. 
+
+%package devel
+Summary: SeqAn development files
+%description devel
+Developer files for SeqAn, in the form for C header files.
+
+%prep
+%setup -q -n seqan-%{version}
+%patch0 -p0
+
+%build
+mkdir -p build/Release && pushd build/Release
+%cmake \
+ -DCMAKE_CXX_FLAGS="$RPM_OPT_FLAGS" \
+ -DCMAKE_C_FLAGS="$RPM_OPT_FLAGS" \
+ -DCMAKE_BUILD_TYPE=Release -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS \
+ -DCMAKE_SKIP_RPATH=YES ../..
+make %{?_smp_mflags}
+make docs
+popd
+
+%install
+%make_install -C build/Release
+
+## Put header files in ad-hoc include directory  
+mkdir -p %{buildroot}%{_includedir}/seqan
+cp -pr extras/include/seqan/* %{buildroot}%{_includedir}/seqan
+cp -pr core/include/seqan/* %{buildroot}%{_includedir}/seqan
+
+## Fixed spurious executable permissions
+find %{buildroot}%{_includedir}/seqan -type f -exec chmod 644 {} \;
+
+## Fix wrong-file-end-of-line-encoding warnings
+sed -i 's/\r$//' %{buildroot}%{_docdir}/seqan/stellar/README
+sed -i 's/\r$//' %{buildroot}%{_docdir}/seqan/breakpoint_calculator/example/alignment.maf
+
+## Rename 'join' binary file; it conflicts with the one owned by 'coreutils' package
+mv %{buildroot}%{_bindir}/join %{buildroot}%{_bindir}/searchjoin
+
+
+%files
+%doc LICENSE README
+%{_bindir}/*
+%doc %{_docdir}/seqan
+
+%files devel
+%doc LICENSE README
+%{_includedir}/seqan/
+
+%changelog
+* Sat Jun 14 2014 Antonio Trande <sagitter at fedoraproject.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 <sagitter at fedoraproject.org> 1.4.1-1
+- First package
diff --git a/sources b/sources
index e69de29..5321f36 100644
--- a/sources
+++ b/sources
@@ -0,0 +1 @@
+5f5fa2e88ef175f60f3cfe374b9d2920  seqan-src-1.4.1.tar.gz