diff options
Diffstat (limited to 'sci-biology/seqan/files')
-rw-r--r-- | sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch | 30 | ||||
-rw-r--r-- | sci-biology/seqan/files/seqan-1.4.2-include.patch | 16 | ||||
-rw-r--r-- | sci-biology/seqan/files/seqan-1.4.2-shared.patch | 22 | ||||
-rw-r--r-- | sci-biology/seqan/files/seqan.pc.in | 10 |
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} |