diff options
Diffstat (limited to 'biology/salmon/files/patch-CMakeLists.txt')
| -rw-r--r-- | biology/salmon/files/patch-CMakeLists.txt | 80 |
1 files changed, 56 insertions, 24 deletions
diff --git a/biology/salmon/files/patch-CMakeLists.txt b/biology/salmon/files/patch-CMakeLists.txt index 5a6bd2de2f02..36038f452843 100644 --- a/biology/salmon/files/patch-CMakeLists.txt +++ b/biology/salmon/files/patch-CMakeLists.txt @@ -1,11 +1,11 @@ ---- CMakeLists.txt.orig 2023-07-21 14:03:31 UTC +--- CMakeLists.txt.orig 2025-07-26 11:52:41 UTC +++ CMakeLists.txt @@ -310,14 +310,16 @@ endif() # Grab pufferfish source --- DURING CONFIGURE TIME! # #### -if(NOT FETCHED_PUFFERFISH) -+ ++# if(NOT FETCHED_PUFFERFISH) +# Fetched by GH_TUPLE in FreeBSD port +# if(NOT FETCHED_PUFFERFISH) exec_program(${CMAKE_CURRENT_SOURCE_DIR}/scripts/fetchPufferfish.sh RETURN_VALUE FETCH_PF_SCRIPT_RET) @@ -19,11 +19,12 @@ ## # Super-secret override -@@ -364,7 +366,10 @@ if(NOT Iconv_IS_BUILT_IN) +@@ -364,7 +366,11 @@ endif() set(ICONV_LIB Iconv::Iconv) endif() -find_package(LibLZMA) ++# find_package(LibLZMA) +# lzma is in FreeBSD base +# find_package(LibLZMA) +set(LIBLZMA_FOUND TRUE) @@ -31,29 +32,35 @@ if(NOT LIBLZMA_FOUND) message("Will attempt to fetch and build liblzma") message("=======================================") -@@ -381,8 +386,8 @@ externalproject_add(liblzma +@@ -381,8 +387,11 @@ externalproject_add(liblzma INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install BUILD_IN_SOURCE TRUE CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS} - BUILD_COMMAND make ${QUIET_MAKE} - INSTALL_COMMAND make ${QUIET_MAKE} install ++# BUILD_COMMAND make ${QUIET_MAKE} ++# INSTALL_COMMAND make ${QUIET_MAKE} install ++# FreeBSD make is bsdmake + BUILD_COMMAND gmake ${QUIET_MAKE} + INSTALL_COMMAND gmake ${QUIET_MAKE} install ) # Tell cmake that the external project generated a library so we can -@@ -411,8 +416,8 @@ externalproject_add(libbz2 +@@ -411,8 +420,11 @@ externalproject_add(libbz2 INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install BUILD_IN_SOURCE TRUE CONFIGURE_COMMAND "" - BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} - INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR> ++# BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ++# INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR> ++# FreeBSD make is bsdmake + BUILD_COMMAND gmake ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} + INSTALL_COMMAND gmake ${QUIET_MAKE} install PREFIX=<INSTALL_DIR> ) # Tell cmake that the external project generated a library so we can # add dependencies here instead of later -@@ -609,9 +614,11 @@ if (NOT CEREAL_FOUND) +@@ -577,9 +589,11 @@ endif() endif() ## Try and find TBB first @@ -68,53 +75,78 @@ if (${TBB_FOUND}) if (${TBB_VERSION} VERSION_GREATER_EQUAL 2021.4) -@@ -791,22 +798,16 @@ endif() +@@ -761,25 +775,28 @@ if (NOT LIBSTADENIO_FOUND) if (NOT LIBSTADENIO_FOUND) message("Build system will compile Staden IOLib") message("==================================================================") + # stadenio is downloaded by GH_TUPLE in FreeBSD port externalproject_add(libstadenio - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-15/io_lib-1.14.15.tar.gz -o staden-io_lib-v1.14.15.tar.gz && -- ${SHASUM} 20814c4365e1e2fe6630fb11d0df370dec4c5688af3871de7f1cb0129671401e staden-io_lib-v1.14.15.tar.gz && -- mkdir -p staden-io_lib-1.14.15 && -- tar -xzf staden-io_lib-v1.14.15.tar.gz --strip-components=1 -C staden-io_lib-1.14.15 && +- DOWNLOAD_COMMAND curl -k -L https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-15-0/io_lib-1.15.0.tar.gz -o staden-io_lib-v1.15.0.tar.gz && +- ${SHASUM} ad343dac7c77086db1b54585c5887b26eda6430d1639d111dd3304c3b749494f staden-io_lib-v1.15.0.tar.gz && +- mkdir -p staden-io_lib-1.15.0 && +- tar -xzf staden-io_lib-v1.15.0.tar.gz --strip-components=1 -C staden-io_lib-1.15.0 && - rm -fr staden-io_lib && -- mv -f staden-io_lib-1.14.15 staden-io_lib +- mv -f staden-io_lib-1.15.0 staden-io_lib && +- curl -k -L https://github.com/samtools/htscodecs/releases/download/v1.6.0/htscodecs-1.6.0.tar.gz -o htscodecs-1.6.0.tar.gz && +- mkdir -p htscodecs-1.6.0 && +- tar -xzf htscodecs-1.6.0.tar.gz --strip-components=1 -C htscodecs-1.6.0 && +- rm -fr staden-io_lib/htscodecs && +- mv -f htscodecs-1.6.0 staden-io_lib/htscodecs ++ # DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external ++ # DOWNLOAD_COMMAND curl -k -L https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-15-0/io_lib-1.15.0.tar.gz -o staden-io_lib-v1.15.0.tar.gz && ++ # ${SHASUM} ad343dac7c77086db1b54585c5887b26eda6430d1639d111dd3304c3b749494f staden-io_lib-v1.15.0.tar.gz && ++ # mkdir -p staden-io_lib-1.15.0 && ++ # tar -xzf staden-io_lib-v1.15.0.tar.gz --strip-components=1 -C staden-io_lib-1.15.0 && ++ # rm -fr staden-io_lib && ++ # mv -f staden-io_lib-1.15.0 staden-io_lib && ++ # curl -k -L https://github.com/samtools/htscodecs/releases/download/v1.6.0/htscodecs-1.6.0.tar.gz -o htscodecs-1.6.0.tar.gz && ++ # mkdir -p htscodecs-1.6.0 && ++ # tar -xzf htscodecs-1.6.0.tar.gz --strip-components=1 -C htscodecs-1.6.0 && ++ # rm -fr staden-io_lib/htscodecs && ++ # mv -f htscodecs-1.6.0 staden-io_lib/htscodecs SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} - BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB} LDFLAGS+=${EXTRA_CMAKE_LIBRARY_FLAGS} CFLAGS+=${EXTRA_CMAKE_INCLUDE_FLAGS} CFLAGS+=${LZFLAG} CFLAGS+=${SCHAR_FLAG} ++ # FreeBSD make is bsdmake + BUILD_COMMAND gmake ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB} LDFLAGS+=${EXTRA_CMAKE_LIBRARY_FLAGS} CFLAGS+=${EXTRA_CMAKE_INCLUDE_FLAGS} CFLAGS+=${LZFLAG} CFLAGS+=${SCHAR_FLAG} - - BUILD_IN_SOURCE 1 - INSTALL_COMMAND make install ++ # FreeBSD make is bsdmake + INSTALL_COMMAND gmake install ) if(NOT LIBLZMA_FOUND) ExternalProject_Add_StepDependencies(libstadenio build liblzma) -@@ -820,23 +821,9 @@ if (ASAN_BUILD) +@@ -793,23 +810,26 @@ else() set(FAST_MALLOC_LIB "") set(HAVE_FAST_MALLOC TRUE) else() - set(FAST_MALLOC_LIB "") - set(HAVE_FAST_MALLOC FALSE) -- -- # See if we have Jemalloc ++ # set(FAST_MALLOC_LIB "") ++ # set(HAVE_FAST_MALLOC FALSE) + + # See if we have Jemalloc - find_package(Jemalloc) - if(Jemalloc_FOUND) -- ## -- # Don't be so stringent about the version yet -- ## -- #if (NOT (${JEMALLOC_VERSION} VERSION_LESS 5.2.1)) ++ # find_package(Jemalloc) ++ # if(Jemalloc_FOUND) + ## + # Don't be so stringent about the version yet + ## + #if (NOT (${JEMALLOC_VERSION} VERSION_LESS 5.2.1)) - message("Found Jemalloc library --- using this memory allocator") - set(FAST_MALLOC_LIB ${JEMALLOC_LIBRARIES}) - set(HAVE_FAST_MALLOC TRUE) -- #else() -- # message("Fond Jemalloc version ${JEMALLOC_VERSION}, but require >= 5.2.1. Downloading newer version") -- #endif() ++ # message("Found Jemalloc library --- using this memory allocator") ++ # set(FAST_MALLOC_LIB ${JEMALLOC_LIBRARIES}) ++ # set(HAVE_FAST_MALLOC TRUE) + #else() + # message("Fond Jemalloc version ${JEMALLOC_VERSION}, but require >= 5.2.1. Downloading newer version") + #endif() - endif() ++ # endif() + # jemalloc is default on FreeBSD + set(FAST_MALLOC_LIB "/usr/lib/libc.so") + set(HAVE_FAST_MALLOC TRUE) |