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|
Description: make RapMap use Debian's versions of dependencies
This involves disabling downloads and adjusting API usage to the versions
packaged in Debian.
Author: Sascha Steinbiss <sascha@steinbiss.name>
--- rapmap.orig/CMakeLists.txt
+++ rapmap/CMakeLists.txt
@@ -215,20 +215,6 @@
endif()
-message("Build system will build libdivsufsort")
-message("==================================================================")
-include(ExternalProject)
-ExternalProject_Add(libdivsufsort
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- URL ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
- BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master/build
- CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR> -DBUILD_DIVSUFSORT64=TRUE -DUSE_OPENMP=TRUE -DBUILD_SHARED_LIBS=FALSE
-)
-set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
-
if (NOT CEREAL_ROOT)
set(CEREAL_ROOT ${GAT_SOURCE_DIR}/external/install)
endif()
@@ -281,24 +267,6 @@
set (JEMALLOC_FLAGS "CC=${CMAKE_C_COMPILER}")
endif()
-if (NOT HAVE_FAST_MALLOC)
- message("Build system will fetch and use JEMalloc")
- message("==================================================================")
- ExternalProject_Add(libjemalloc
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/4.5.0.tar.gz -o jemalloc-4.5.0.tar.gz &&
- tar -xzf jemalloc-4.5.0.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-4.5.0
- BUILD_IN_SOURCE TRUE
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND sh -c "${JEMALLOC_FLAGS} ./autogen.sh --disable-debug --prefix=<INSTALL_DIR>"
- INSTALL_COMMAND cp -r lib <INSTALL_DIR>/ && cp -r include <INSTALL_DIR>/
- )
-
- set (FAST_MALLOC_LIB ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libjemalloc.a)
- set (HAVE_FAST_MALLOC TRUE)
-endif ()
-
###
#
# Done building external dependencies.
--- rapmap.orig/src/CMakeLists.txt
+++ rapmap/src/CMakeLists.txt
@@ -63,8 +63,8 @@
add_executable(rapmap ${RAPMAP_MAIN_SRCS})
# our suffix array construction libraries
-set (SUFFARRAY_LIB ${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a)
-set (SUFFARRAY64_LIB ${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a)
+set (SUFFARRAY_LIB divsufsort)
+set (SUFFARRAY64_LIB divsufsort64)
# build KSW2 library
set (KSW2PP_BASIC_LIB_SRCS
|
