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biology/spoa: update 4.0.7 → 4.1.0

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Reported by:	portscout
This commit is contained in:
Yuri Victorovich 2023-08-29 08:49:03 -07:00
parent f40164d18b
commit e06be01f1e
4 changed files with 21 additions and 128 deletions
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18
biology/spoa/Makefile
View file

@ -1,6 +1,5 @@
PORTNAME= spoa
DISTVERSION= 4.0.7
PORTREVISION= 4
DISTVERSION= 4.1.0
CATEGORIES= biology
MAINTAINER= yuri@FreeBSD.org
@ -11,7 +10,7 @@ LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= bioparser>0:biology/bioparser \
${LOCALBASE}/include/biosoup/nucleic_acid.hpp:biology/biosoup \
biosoup>0:biology/biosoup \
cereal>0:devel/cereal \
simde>0:devel/simde
LIB_DEPENDS= libcpu_features.so:devel/cpu_features
@ -24,8 +23,17 @@ USE_LDCONFIG= yes
USE_GITHUB= yes
GH_ACCOUNT= rvaser
CMAKE_ON= BUILD_SHARED_LIBS spoa_optimize_for_portability spoa_build_executable spoa_use_simde spoa_use_simde_nonvec spoa_use_simde_openmp
CMAKE_OFF= spoa_optimize_for_native
CMAKE_ON= BUILD_SHARED_LIBS \
spoa_build_exe \
spoa_optimize_for_portability \
spoa_build_executable \
spoa_use_simde \
spoa_use_simde_nonvec \
spoa_use_simde_openmp \
spoa_use_cereal \
spoa_use_simde_openmp
CMAKE_OFF= spoa_optimize_for_native \
spoa_build_tests
CXXFLAGS+= -I${LOCALBASE}/include/cpu_features
LDFLAGS+= -lz -lcpu_features

6
biology/spoa/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1611045674
SHA256 (rvaser-spoa-4.0.7_GH0.tar.gz) = f8cb409adcca20ca6cc0025371743b915790879957cf001ca5e155ed16fd14e0
SIZE (rvaser-spoa-4.0.7_GH0.tar.gz) = 43574
TIMESTAMP = 1693289273
SHA256 (rvaser-spoa-4.1.0_GH0.tar.gz) = 43238356f00bce2ad9698fc18b3e320024172a82182dcff24d57c5cf19e342c8
SIZE (rvaser-spoa-4.1.0_GH0.tar.gz) = 47814

118
biology/spoa/files/patch-CMakeLists.txt
View file

@ -1,118 +0,0 @@
--- CMakeLists.txt.orig 2021-01-15 03:44:02 UTC
+++ CMakeLists.txt
@@ -44,9 +44,10 @@ if (spoa_use_simde OR
endif ()
endif ()
-if (NOT TARGET cereal)
- add_subdirectory(vendor/cereal EXCLUDE_FROM_ALL)
-endif ()
+#if (NOT TARGET cereal)
+# add_subdirectory(vendor/cereal EXCLUDE_FROM_ALL)
+#endif ()
+find_package(cereal REQUIRED)
add_library(${PROJECT_NAME}
src/alignment_engine.cpp
@@ -55,19 +56,19 @@ add_library(${PROJECT_NAME}
src/dispatcher.cpp)
target_include_directories(${PROJECT_NAME} PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde>
- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/cpu_features/include>
+ #$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde>
+ #$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/cpu_features/include>
$<INSTALL_INTERFACE:include>)
target_link_libraries(${PROJECT_NAME}
- cereal)
+ cereal::cereal)
if (BUILD_SHARED_LIBS)
set_property(TARGET ${PROJECT_NAME} PROPERTY SOVERSION "7.0.0")
endif ()
if (spoa_generate_dispatch)
- if (NOT TARGET cpu_features)
- add_subdirectory(vendor/cpu_features EXCLUDE_FROM_ALL)
- endif ()
+ #if (NOT TARGET cpu_features)
+ # add_subdirectory(vendor/cpu_features EXCLUDE_FROM_ALL)
+ #endif ()
list(APPEND ARCHITECTURES avx2 sse4.1 sse2)
foreach(arch IN LISTS ARCHITECTURES)
@@ -78,7 +79,7 @@ if (spoa_generate_dispatch)
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde>
$<INSTALL_INTERFACE:include>)
target_link_libraries(${PROJECT_NAME}_${arch}
- cereal)
+ cereal::cereal)
set_target_properties(${PROJECT_NAME}_${arch} PROPERTIES
COMPILE_FLAGS "-m${arch}")
if (BUILD_SHARED_LIBS)
@@ -92,8 +93,8 @@ if (spoa_generate_dispatch)
${PROJECT_NAME}_sse4.1
${PROJECT_NAME}_sse2)
- target_link_libraries(${PROJECT_NAME}
- cpu_features)
+ #target_link_libraries(${PROJECT_NAME}
+ # cpu_features)
endif ()
include(GNUInstallDirs)
@@ -110,18 +111,19 @@ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/spoa-1.pc
option(spoa_build_executable "Build spoa standalone tool" OFF)
if (spoa_build_executable)
- if (NOT TARGET biosoup)
- add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL)
- endif ()
- if (NOT TARGET bioparser)
- add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
- endif ()
+ #if (NOT TARGET biosoup)
+ # add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL)
+ #endif ()
+ #if (NOT TARGET bioparser)
+ # add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
+ #endif ()
add_executable(${PROJECT_NAME}_exe
src/main.cpp)
target_link_libraries(${PROJECT_NAME}_exe
${PROJECT_NAME}
- bioparser
- biosoup)
+ #bioparser
+ #biosoup
+ )
target_compile_definitions(${PROJECT_NAME}_exe PRIVATE
SPOA_VERSION="v${PROJECT_VERSION}")
set_property(TARGET ${PROJECT_NAME}_exe PROPERTY
@@ -134,19 +136,19 @@ endif ()
option(spoa_build_tests "Build spoa unit tests" OFF)
if (spoa_build_tests)
find_package(GTest REQUIRED)
- if (NOT TARGET biosoup)
- add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL)
- endif ()
- if (NOT TARGET bioparser)
- add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
- endif ()
+ #if (NOT TARGET biosoup)
+ # add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL)
+ #endif ()
+ #if (NOT TARGET bioparser)
+ # add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
+ #endif ()
include_directories(${PROJECT_SOURCE_DIR}/src)
add_executable(${PROJECT_NAME}_test
test/spoa_test.cpp)
target_link_libraries(${PROJECT_NAME}_test
${PROJECT_NAME}
- bioparser
- biosoup
+ #bioparser
+ #biosoup
GTest::Main)
target_compile_definitions(${PROJECT_NAME}_test PRIVATE
SPOA_DATA_PATH="${PROJECT_SOURCE_DIR}/test/data/sample.fastq.gz")

7
biology/spoa/pkg-plist
View file

@ -1,8 +1,11 @@
bin/spoa
include/spoa/alignment_engine.hpp
include/spoa/architectures.hpp
include/spoa/graph.hpp
include/spoa/spoa.hpp
include/spoa/version.hpp
lib/cmake/spoa/spoaConfig.cmake
lib/cmake/spoa/spoaConfigVersion.cmake
lib/cmake/spoa/spoaTargets-%%CMAKE_BUILD_TYPE%%.cmake
lib/cmake/spoa/spoaTargets.cmake
lib/libspoa.so
lib/libspoa.so.7.0.0
libdata/pkgconfig/spoa-1.pc