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freebsd-ports/biology/salmon/files/patch-CMakeLists.txt
Jason W. Bacon 64a6421c24 biology/salmon: Transcript-level quantification of RNA-seq 
Salmon is a wicked-fast program to produce a highly-accurate,
transcript-level quantification estimates from RNA-seq data. Salmon
achieves is accuracy and speed via a number of different innovations,
including the use of quasi-mapping (accurate but fast-to-compute
proxies for traditional read alignments), and massively-parallel
stochastic collapsed variational inference. The result is a versatile
tool that fits nicely into many differnt pipelines.
2023-07-21 18:06:36 -05:00

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--- CMakeLists.txt.orig 2023-07-21 14:03:31 UTC
+++ CMakeLists.txt
@@ -310,14 +310,16 @@ endif()
# Grab pufferfish source --- DURING CONFIGURE TIME!
#
####
-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)
message(STATUS "fetch PUFFERFISH exit code ${FETCH_PF_SCRIPT_RET}")
if(NOT (FETCH_PF_SCRIPT_RET EQUAL 0))
message(FATAL_ERROR "Could not fetch pufferfish source [fetchPufferfish.sh returned exit code ${FETCH_PF_SCRIPT_RET}].")
endif()
set(FETCHED_PUFFERFISH TRUE CACHE BOOL "Has pufferfish been fetched?" FORCE)
-endif()
+# endif()
##
# Super-secret override
@@ -364,7 +366,10 @@ if(NOT Iconv_IS_BUILT_IN)
set(ICONV_LIB Iconv::Iconv)
endif()
-find_package(LibLZMA)
+# lzma is in FreeBSD base
+# find_package(LibLZMA)
+set(LIBLZMA_FOUND TRUE)
+set(LIBLZMA_LIBRARIES /usr/lib/liblzma.a /usr/lib/libmd.a)
if(NOT LIBLZMA_FOUND)
message("Will attempt to fetch and build liblzma")
message("=======================================")
@@ -381,8 +386,8 @@ 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 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
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 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)
endif()
## Try and find TBB first
-find_package(TBB 2021.4
- HINTS ${TBB_ROOT_SEARCH}
- COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
+# find_package(TBB 2021.4
+# HINTS ${TBB_ROOT_SEARCH}
+# COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
+# tbbmalloc_proxy is rolled into tbbmalloc in FreeBSD ports
+find_package(TBB 2021.4 COMPONENTS tbb tbbmalloc)
if (${TBB_FOUND})
if (${TBB_VERSION} VERSION_GREATER_EQUAL 2021.4)
@@ -791,22 +798,16 @@ endif()
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 &&
- rm -fr staden-io_lib &&
- mv -f staden-io_lib-1.14.15 staden-io_lib
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}
+ 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+=${SCHAR_FLAG}
BUILD_IN_SOURCE 1
- INSTALL_COMMAND make install
+ INSTALL_COMMAND gmake install
)
if(NOT LIBLZMA_FOUND)
ExternalProject_Add_StepDependencies(libstadenio build liblzma)
@@ -820,23 +821,9 @@ if (ASAN_BUILD)
set(FAST_MALLOC_LIB "")
set(HAVE_FAST_MALLOC TRUE)
else()
- set(FAST_MALLOC_LIB "")
- set(HAVE_FAST_MALLOC FALSE)
-
- # See if we have Jemalloc
- find_package(Jemalloc)
- if(Jemalloc_FOUND)
- ##
- # Don't be so stringent about the version yet
- ##
- #if (NOT (${JEMALLOC_VERSION} VERSION_LESS 5.2.1))
- 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()
+ # jemalloc is default on FreeBSD
+ set(FAST_MALLOC_LIB "/usr/lib/libc.so")
+ set(HAVE_FAST_MALLOC TRUE)
endif()
if(CONDA_BUILD)
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