[med-svn] [salmon] 08/09: Revert commit of patched files
Andreas Tille
tille at debian.org
Tue Aug 30 10:12:30 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository salmon.
commit 6a5bda8646d38fd54dfc7dfd72729c569a06cec9
Author: Andreas Tille <tille at debian.org>
Date: Tue Aug 30 12:06:21 2016 +0200
Revert commit of patched files
---
CMakeLists.txt | 348 ++++++++++++++++++++++++-------------------------
src/CMakeLists.txt | 22 +++-
src/Salmon.cpp | 8 +-
src/SalmonQuantify.cpp | 2 +-
4 files changed, 192 insertions(+), 188 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 14b9cc8..0a6ec55 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
set (WARNING_IGNORE_FLAGS "-Wno-deprecated-register")
set (BOOST_CXX_FLAGS "-Wno-deprecated-register -std=c++11")
## Prefer static to dynamic libraries
-# SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
+SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
## Set the standard required compile flags
# Nov 18th --- removed -DHAVE_CONFIG_H
@@ -176,13 +176,10 @@ endif ( DEFINED CUSTOM_BOOST_PATH )
##
# We want static, multithreaded boost libraries
##
-set (Boost_USE_STATIC_LIBS OFF)
+set (Boost_USE_STATIC_LIBS ON)
set (Boost_USE_MULTITHREADED ON)
#set (Boost_USE_STATIC_RUNTIME OFF)
-find_package (PkgConfig)
-pkg_check_modules(TBB REQUIRED tbb)
-
find_package (ZLIB)
if (NOT ZLIB_FOUND)
message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
@@ -240,7 +237,7 @@ endif()
# Set the latest version and look for what we need
##
set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58" "1.59" "1.60" "1.61")
-find_package(Boost 1.53.0 COMPONENTS filesystem system thread timer program_options)
+find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
message("Boost_FOUND = ${Boost_FOUND}")
@@ -350,153 +347,152 @@ ExternalProject_Add(libdivsufsort
)
set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
-#message("Build system will fetch and build the Cereal serialization library")
-#message("==================================================================")
-#include(ExternalProject)
-#ExternalProject_Add(libcereal
-# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-# DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz -o cereal-v1.1.2.tar.gz &&
-# tar -xzvf cereal-v1.1.2.tar.gz
-# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2
-# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-# UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
-# BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2/build
-# CONFIGURE_COMMAND ""
-# BUILD_COMMAND ""
-# INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/include && cp -r <SOURCE_DIR>/include/cereal <INSTALL_DIR>/include"
-#)
-#
-#message("Build system will fetch and build BWA (for Salmon)")
-#message("==================================================================")
-#include(ExternalProject)
-#ExternalProject_Add(libbwa
-# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -o bwa-master.tar.gz &&
-# mkdir -p bwa-master &&
-# tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
-# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
-# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-# CONFIGURE_COMMAND ""
-# BUILD_COMMAND sh -c "make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}"
-# INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/lib && mkdir -p <INSTALL_DIR>/include/bwa && cp libbwa.a <INSTALL_DIR>/lib && cp *.h <INSTALL_DIR>/include/bwa && cp is.c bwtindex.c bwt_gen.c QSufSort.c ${CMAKE_CURRENT_SOURCE_DIR}/src/"
-# BUILD_IN_SOURCE TRUE
-#)
-#
-#find_package(Jellyfish 2.2.6)
-#
-#if (NOT JELLYFISH_FOUND)
-#message("Build system will fetch and build Jellyfish")
-#message("==================================================================")
-#ExternalProject_Add(libjellyfish
-# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-# DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz -o jellyfish-2.2.6.tgz &&
-# rm -fr jellyfish-2.2.6 &&
-# tar -xzvf jellyfish-2.2.6.tgz
-# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6
-# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-# CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-# BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-# BUILD_IN_SOURCE 1
-# INSTALL_COMMAND make install
-#)
-#endif()
-
-#find_package(TBB)
+message("Build system will fetch and build the Cereal serialization library")
+message("==================================================================")
+include(ExternalProject)
+ExternalProject_Add(libcereal
+ DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+ DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz -o cereal-v1.1.2.tar.gz &&
+ tar -xzvf cereal-v1.1.2.tar.gz
+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2
+ INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+ UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
+ BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2/build
+ CONFIGURE_COMMAND ""
+ BUILD_COMMAND ""
+ INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/include && cp -r <SOURCE_DIR>/include/cereal <INSTALL_DIR>/include"
+)
+
+message("Build system will fetch and build BWA (for Salmon)")
+message("==================================================================")
+include(ExternalProject)
+ExternalProject_Add(libbwa
+ DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+ DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -o bwa-master.tar.gz &&
+ mkdir -p bwa-master &&
+ tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
+ INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+ CONFIGURE_COMMAND ""
+ BUILD_COMMAND sh -c "make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}"
+ INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/lib && mkdir -p <INSTALL_DIR>/include/bwa && cp libbwa.a <INSTALL_DIR>/lib && cp *.h <INSTALL_DIR>/include/bwa && cp is.c bwtindex.c bwt_gen.c QSufSort.c ${CMAKE_CURRENT_SOURCE_DIR}/src/"
+ BUILD_IN_SOURCE TRUE
+)
+find_package(Jellyfish 2.2.6)
+
+if (NOT JELLYFISH_FOUND)
+message("Build system will fetch and build Jellyfish")
+message("==================================================================")
+ExternalProject_Add(libjellyfish
+ DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+ DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz -o jellyfish-2.2.6.tgz &&
+ rm -fr jellyfish-2.2.6 &&
+ tar -xzvf jellyfish-2.2.6.tgz
+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6
+ INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+ CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
+ BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
+ BUILD_IN_SOURCE 1
+ INSTALL_COMMAND make install
+)
+endif()
+
+find_package(TBB)
##
#
# Fetch and build Intel's Threading Building Blocks library.
#
##
-#if(NOT TBB_FOUND)
+if(NOT TBB_FOUND)
-#set(TBB_WILL_RECONFIGURE TRUE)
+set(TBB_WILL_RECONFIGURE TRUE)
# Set the appropriate compiler
-#if (CLANG)
-# set(TBB_COMPILER "clang")
-#else()
-# set(TBB_COMPILER "gcc")
-#endif()
-
-#message("Build system will fetch and build Intel Threading Building Blocks")
-#message("==================================================================")
-## These are useful for the custom install step we'll do later
-#set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss)
-#set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
-
-#if ("${TBB_COMPILER}" STREQUAL "gcc")
+if (CLANG)
+ set(TBB_COMPILER "clang")
+else()
+ set(TBB_COMPILER "gcc")
+endif()
+
+message("Build system will fetch and build Intel Threading Building Blocks")
+message("==================================================================")
+# These are useful for the custom install step we'll do later
+set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss)
+set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
+
+if ("${TBB_COMPILER}" STREQUAL "gcc")
## Don't know why it's a problem yet, but if we're using
## GCC, get rid of the DO_ITT_NOTIFY flag
set(TBB_CXXFLAGS "${TBB_CXXFLAGS} -UDO_ITT_NOTIFY")
-#endif()
-
-#ExternalProject_Add(libtbb
-# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-# URL https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160526oss_src_0.tgz
-# DOWNLOAD_COMMAND curl -k -L https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160526oss_src_0.tgz -o tbb_20160526oss_src.tgz &&
-# tar -xzvf tbb_20160526oss_src.tgz
-# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss
-# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-# PATCH_COMMAND "${TBB_PATCH_STEP}"
-# CONFIGURE_COMMAND ""
-# BUILD_COMMAND make CXXFLAGS=${TBB_CXXFLAGS} lambdas=1 compiler=${TBB_COMPILER} cfg=release tbb_build_prefix=LIBS
-# INSTALL_COMMAND sh -c "cp ${TBB_SOURCE_DIR}/build/LIBS_release/*.${SHARED_LIB_EXTENSION}* ${TBB_INSTALL_DIR}/lib && cp -r ${TBB_SOURCE_DIR}/include/* ${TBB_INSTALL_DIR}/include"
-# BUILD_IN_SOURCE 1
-#)
-
-#SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DTBB_WILL_RECONFIGURE=FALSE -DTBB_RECONFIGURE=TRUE)
-#ExternalProject_Add_Step(libtbb reconfigure
-# COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
-# DEPENDEES install
-#)
-#endif()
+endif()
+
+ExternalProject_Add(libtbb
+ DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+ URL https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160526oss_src_0.tgz
+ DOWNLOAD_COMMAND curl -k -L https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160526oss_src_0.tgz -o tbb_20160526oss_src.tgz &&
+ tar -xzvf tbb_20160526oss_src.tgz
+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss
+ INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+ PATCH_COMMAND "${TBB_PATCH_STEP}"
+ CONFIGURE_COMMAND ""
+ BUILD_COMMAND make CXXFLAGS=${TBB_CXXFLAGS} lambdas=1 compiler=${TBB_COMPILER} cfg=release tbb_build_prefix=LIBS
+ INSTALL_COMMAND sh -c "cp ${TBB_SOURCE_DIR}/build/LIBS_release/*.${SHARED_LIB_EXTENSION}* ${TBB_INSTALL_DIR}/lib && cp -r ${TBB_SOURCE_DIR}/include/* ${TBB_INSTALL_DIR}/include"
+ BUILD_IN_SOURCE 1
+)
+
+SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DTBB_WILL_RECONFIGURE=FALSE -DTBB_RECONFIGURE=TRUE)
+ExternalProject_Add_Step(libtbb reconfigure
+ COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
+ DEPENDEES install
+)
+endif()
##
# If we're fetching tbb, we need to have dummy paths for these variables
# so that CMake won't complain
##
-#if(TBB_WILL_RECONFIGURE)
-# set(TBB_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
-# set(TBB_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
-# #set(TBB_LIBRARIES tbb tbbmalloc)
-# set(TBB_LIBRARIES ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libtbb.${SHARED_LIB_EXTENSION}
-# ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libtbbmalloc.${SHARED_LIB_EXTENSION}
-# )
-#endif()
+if(TBB_WILL_RECONFIGURE)
+ set(TBB_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
+ set(TBB_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
+ #set(TBB_LIBRARIES tbb tbbmalloc)
+ set(TBB_LIBRARIES ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libtbb.${SHARED_LIB_EXTENSION}
+ ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libtbbmalloc.${SHARED_LIB_EXTENSION}
+ )
+endif()
##
# Similar to the Boost trick above, the libtbb reconfigure should force this code
# to be run on the second configuration pass, where it should appropriately set the
# TBB_INSTALL_DIR variable.
##
-#if (TBB_RECONFIGURE)
-# unset(TBB_FOUND CACHE)
-# unset(TBB_INSTALL_DIR CACHE)
-# unset(CMAKE_PREFIX_PATH CACHE)
-# set(CMAKE_PREFIX_PATH ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
-# set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
-# message("TBB_INSTALL_DIR = ${TBB_INSTALL_DIR}")
-# find_package(TBB)
-#endif()
+if (TBB_RECONFIGURE)
+ unset(TBB_FOUND CACHE)
+ unset(TBB_INSTALL_DIR CACHE)
+ unset(CMAKE_PREFIX_PATH CACHE)
+ set(CMAKE_PREFIX_PATH ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
+ set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
+ message("TBB_INSTALL_DIR = ${TBB_INSTALL_DIR}")
+ find_package(TBB)
+endif()
message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
-#message("Build system will compile libgff")
-#message("==================================================================")
-#ExternalProject_Add(libgff
-# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-# DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz &&
-# tar -xzvf libgff.tgz &&
-# rm -fr libgff &&
-# mv libgff-1.0 libgff
-# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
-# UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
-# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-# BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff/build
-# CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_SOURCE_DIR}/external/install
-#)
+message("Build system will compile libgff")
+message("==================================================================")
+ExternalProject_Add(libgff
+ DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+ DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz &&
+ tar -xzvf libgff.tgz &&
+ rm -fr libgff &&
+ mv libgff-1.0 libgff
+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
+ UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
+ INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+ BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff/build
+ CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_SOURCE_DIR}/external/install
+)
# Because of the way that Apple has changed SIP
# in el capitan, some headers may be in a new location
@@ -506,39 +502,39 @@ if (APPLE)
endif()
-#message("Build system will compile Staden IOLib")
-#message("==================================================================")
-#ExternalProject_Add(libstadenio
-# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/releases/download/v1.13.10/io_lib-1.13.10.tar.gz -o staden-io_lib-v1.13.10.tar.gz &&
-# mkdir -p staden-io_lib-1.13.10 &&
-# tar -xzf staden-io_lib-v1.13.10.tar.gz --strip-components=1 -C staden-io_lib-1.13.10 &&
-# rm -fr staden-io_lib &&
-# mv -f staden-io_lib-1.13.10 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=${CMAKE_CXX_COMPILER}
-# BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB}
-#
-# BUILD_IN_SOURCE 1
-# INSTALL_COMMAND make install
-#)
-
-#message("Build system will fetch SPDLOG")
-#message("==================================================================")
-#ExternalProject_Add(libspdlog
-# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.0.1.tar.gz -o spdlog-v1.0.1.tar.gz &&
-# tar -xzf spdlog-v1.0.1.tar.gz &&
-# rm -fr spdlog &&
-# mv -f spdlog-1.0.1 spdlog
-# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog
-# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-# CONFIGURE_COMMAND ""
-# BUILD_COMMAND ""
-# BUILD_IN_SOURCE 1
-# INSTALL_COMMAND cp -r <SOURCE_DIR>/include/spdlog <INSTALL_DIR>/include
-#)
+message("Build system will compile Staden IOLib")
+message("==================================================================")
+ExternalProject_Add(libstadenio
+ DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+ DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/releases/download/v1.13.10/io_lib-1.13.10.tar.gz -o staden-io_lib-v1.13.10.tar.gz &&
+ mkdir -p staden-io_lib-1.13.10 &&
+ tar -xzf staden-io_lib-v1.13.10.tar.gz --strip-components=1 -C staden-io_lib-1.13.10 &&
+ rm -fr staden-io_lib &&
+ mv -f staden-io_lib-1.13.10 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=${CMAKE_CXX_COMPILER}
+ BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB}
+
+ BUILD_IN_SOURCE 1
+ INSTALL_COMMAND make install
+)
+
+message("Build system will fetch SPDLOG")
+message("==================================================================")
+ExternalProject_Add(libspdlog
+ DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+ DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.0.1.tar.gz -o spdlog-v1.0.1.tar.gz &&
+ tar -xzf spdlog-v1.0.1.tar.gz &&
+ rm -fr spdlog &&
+ mv -f spdlog-1.0.1 spdlog
+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog
+ INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+ CONFIGURE_COMMAND ""
+ BUILD_COMMAND ""
+ BUILD_IN_SOURCE 1
+ INSTALL_COMMAND cp -r <SOURCE_DIR>/include/spdlog <INSTALL_DIR>/include
+)
set (FAST_MALLOC_LIB "")
set (HAVE_FAST_MALLOC FALSE)
@@ -562,23 +558,23 @@ if (NOT HAVE_FAST_MALLOC)
endif()
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/4.0.4.tar.gz -o jemalloc-4.0.4.tar.gz &&
-# tar -xzf jemalloc-4.0.4.tar.gz
-# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-4.0.4
-# BUILD_IN_SOURCE TRUE
-# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-# CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} ./autogen.sh --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 ()
+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/4.0.4.tar.gz -o jemalloc-4.0.4.tar.gz &&
+ tar -xzf jemalloc-4.0.4.tar.gz
+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-4.0.4
+ BUILD_IN_SOURCE TRUE
+ INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+ CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} ./autogen.sh --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 ()
##
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index ee1b87a..f31a927 100755
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,7 +1,11 @@
include_directories(
${GAT_SOURCE_DIR}/include
-/usr/include/eigen3
-/usr/include/bwa
+${GAT_SOURCE_DIR}/include/eigen3
+${GAT_SOURCE_DIR}/external
+${GAT_SOURCE_DIR}/external/cereal/include
+${GAT_SOURCE_DIR}/external/install/include
+${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.2.6
+${GAT_SOURCE_DIR}/external/install/include/bwa
${ZLIB_INCLUDE_DIR}
${TBB_INCLUDE_DIRS}
${Boost_INCLUDE_DIRS}
@@ -103,7 +107,7 @@ else()
endif()
# Build the Salmon library
-add_library(salmon_core ${SALMON_LIB_SRCS} )
+add_library(salmon_core STATIC ${SALMON_LIB_SRCS} )
# Build the salmon executable
add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
@@ -127,19 +131,23 @@ target_link_libraries(salmon
gff
${PTHREAD_LIB}
${Boost_LIBRARIES}
- libstaden-read.so
+ ${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a
${ZLIB_LIBRARY}
${SUFFARRAY_LIB}
${SUFFARRAY64_LIB}
- libjellyfish-2.0.so
- /usr/lib/libbwa.a
+ ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a
+ ${GAT_SOURCE_DIR}/external/install/lib/libbwa.a
m
- tbb
+ ${LIBLZMA_LIBRARIES}
+ ${BZIP2_LIBRARIES}
+ ${TBB_LIBRARIES}
${LIBSALMON_LINKER_FLAGS}
${NON_APPLECLANG_LIBS}
${FAST_MALLOC_LIB}
)
+add_dependencies(salmon libbwa)
+
# Link the executable
target_link_libraries(unitTests
salmon_core
diff --git a/src/Salmon.cpp b/src/Salmon.cpp
index 1f11b9b..ffaf8c2 100644
--- a/src/Salmon.cpp
+++ b/src/Salmon.cpp
@@ -181,10 +181,10 @@ int main( int argc, char* argv[] ) {
std::exit(0);
}
- //if (!vm.count("no-version-check")){
- // std::string versionMessage = getVersionMessage();
- // std::cerr << versionMessage;
- //}
+ if (!vm.count("no-version-check")){
+ std::string versionMessage = getVersionMessage();
+ std::cerr << versionMessage;
+ }
po::notify(vm);
diff --git a/src/SalmonQuantify.cpp b/src/SalmonQuantify.cpp
index be14e92..c88940e 100644
--- a/src/SalmonQuantify.cpp
+++ b/src/SalmonQuantify.cpp
@@ -1985,7 +1985,7 @@ int salmonQuantify(int argc, char* argv[]) {
(
"maxOcc,m",
po::value<int>(&(memOptions->max_occ))->default_value(200),
- "(S)MEMs occurring more than this many times won't be considered.")
+ "(S)MEMs occuring more than this many times won't be considered.")
(
"initUniform", po::bool_switch(&(sopt.initUniform))->default_value(false),
"initialize the offline inference with uniform parameters, rather than seeding with online parameters.")
--
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