reinit the tree, so we can have metadata

4 files changed, 78 insertions, 0 deletions

diff --git a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
new file mode 100644
index 000000000000..4c7893e90c05
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
@@ -0,0 +1,30 @@
+Add default disabled flag to enable generation of documentation.
+For SeqAn 1.4.2 we generally do not want docs, as 1.4.2 is only a
+support library for legacy tools.
+
+--- seqan-1.4.2/CMakeLists.txt
++++ seqan-1.4.2/CMakeLists.txt
+@@ -123,10 +123,12 @@
+ add_subdirectory (core)
+ message (STATUS "Configuring extras")
+ add_subdirectory (extras)
++if (NOT SEQAN_NO_DOX)
+ message (STATUS "Configuring docs")
+ add_subdirectory (docs)
+ message (STATUS "Configuring manual")
+ add_subdirectory (manual)
++endif ()
+ message (STATUS "Configuring sandbox")
+ add_subdirectory (sandbox)
+ message (STATUS "Configuring util/py_lib")
+--- seqan-1.4.2/docs/main.py
++++ seqan-1.4.2/docs/main.py
+@@ -123,7 +123,7 @@
+ 
+         # Done, print end message.
+         print 'Documentation created/updated.'
+-        return dddoc_html.WARNING_COUNT > 0
++        return 0
+     
+     
+ def main(argv):
diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch
new file mode 100644
index 000000000000..5baee4d8ebc0
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-include.patch
@@ -0,0 +1,16 @@
+ core/include/seqan/index/index_qgram_openaddressing.h | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h
+index 4a6c2e6..8cc9a42 100644
+--- a/core/include/seqan/index/index_qgram_openaddressing.h
++++ b/core/include/seqan/index/index_qgram_openaddressing.h
+@@ -35,6 +35,8 @@
+ #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+ #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+ 
++#include <smmintrin.h>
++
+ namespace SEQAN_NAMESPACE_MAIN
+ {
+ 
diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
new file mode 100644
index 000000000000..0f438ff07bce
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
@@ -0,0 +1,22 @@
+ util/cmake/SeqAnBuildSystem.cmake | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
+index bcba2c0..d53cd01 100644
+--- a/util/cmake/SeqAnBuildSystem.cmake
++++ b/util/cmake/SeqAnBuildSystem.cmake
+@@ -144,10 +144,10 @@ macro (seqan_register_apps)
+     set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
+ 
+     # enable static linkage for seqan apps
+-    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
+-      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+-      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+-    endif ()
++#    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
++#      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
++#      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
++#    endif ()
+ 
+     # Get all direct entries of the current source directory into ENTRIES.
+     file (GLOB ENTRIES
diff --git a/sci-biology/seqan/files/seqan.pc.in b/sci-biology/seqan/files/seqan.pc.in
new file mode 100644
index 000000000000..f917faef8ba3
--- /dev/null
+++ b/sci-biology/seqan/files/seqan.pc.in
@@ -0,0 +1,10 @@
+prefix=@CMAKE_INSTALL_PREFIX@
+exec_prefix=${prefix}
+includedir=${prefix}/include
+
+Name: @CMAKE_PROJECT_NAME@
+Description: C++ library for biological sequence analysis
+URL: http://www.seqan.de
+Version: @SEQAN_VERSION_STRING@
+Requires: zlib
+Cflags: -I${includedir}