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--- salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:49.275828719 +0200
+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:38.945565690 +0200
@@ -235,31 +235,7 @@
find_package (LibLZMA)
if (NOT LIBLZMA_FOUND)
- message ("Will attempt to fetch and build liblzma")
- message ("=======================================")
-ExternalProject_Add(liblzma
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- ##
- DOWNLOAD_COMMAND curl -k -L http://tukaani.org/xz/xz-5.2.2.tar.gz -o xz-5.2.2.tar.gz &&
- ${SHASUM} 73df4d5d34f0468bd57d09f2d8af363e95ed6cc3a4a86129d2f2c366259902a2 xz-5.2.2.tar.gz &&
- tar -xzvf xz-5.2.2.tar.gz
- #URL http://tukaani.org/xz/xz-5.2.2.tar.gz
- #URL_HASH SHA1=14663612422ab61386673be78fbb2556f50a1f08
- ##
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2
- 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
-)
-
-# Tell cmake that the external project generated a library so we can
-# add dependencies here instead of later
-set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
-set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
-set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
-set (FETCHED_LIBLZMA TRUE)
+ message (FATAL_ERROR "liblzma must be installed before configuration & building can proceed")
else()
message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
message("===========================================")
@@ -267,28 +243,7 @@
find_package (BZip2)
if (NOT BZIP2_FOUND)
- message ("Will attempt to fetch and build libbz2")
- message ("=======================================")
-ExternalProject_Add(libbz2
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -o bzip2-1.0.6.tar.gz &&
- ${SHASUM} a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd bzip2-1.0.6.tar.gz &&
- tar -xzvf bzip2-1.0.6.tar.gz
- #URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
- #URL_HASH SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6
- 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>
-)
-# Tell cmake that the external project generated a library so we can
-# add dependencies here instead of later
-set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
-set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
-set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
-set (FETCHED_LIBBZ2 TRUE)
+ message (FATAL_ERROR "libbz2 must be installed before configuration & building can proceed")
else()
message("Found libbz2 library: ${BZIP2_LIBRARIES}")
message("===========================================")
@@ -333,61 +288,15 @@
# Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST
# option, go and grab it for them.
##
-if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST))
+if (NOT Boost_FOUND)
message(FATAL_ERROR
"Salmon cannot be compiled without Boost.\n"
"It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n"
"This build system can also download and install a local version of boost for you (this takes a lot of time).\n"
"To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE"
)
-elseif(FETCH_BOOST)
- ## Let the rest of the build process know we're going to be fetching boost
- set (BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception
- --with-filesystem --with-graph --with-graph_parallel --with-math
- --with-program_options --with-system --with-thread
- --with-timer)
- set (BOOST_WILL_RECONFIGURE TRUE)
- set (FETCH_BOOST FALSE)
- message("Build system will fetch and build Boost")
- message("==================================================================")
- ExternalProject_Add(libboost
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L http://downloads.sourceforge.net/project/boost/boost/1.66.0/boost_1_66_0.tar.gz -o boost_1_66_0.tar.gz &&
- ${SHASUM} bd0df411efd9a585e5a2212275f8762079fed8842264954675a4fddc46cfcf60 boost_1_66_0.tar.gz &&
- tar xzf boost_1_66_0.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR>
- BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install
- BUILD_IN_SOURCE 1
- INSTALL_COMMAND ""
- )
-
- ##
- # After we've installed boost,
- ##
- SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE)
- ExternalProject_Add_Step(libboost reconfigure
- COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
- DEPENDEES install
- )
- set (FETCHED_BOOST TRUE)
endif()
-##
-# If we're fetching boost and we need to have dummy paths for these variables
-# so that CMake won't complain
-##
-if (BOOST_WILL_RECONFIGURE)
- message("Setting Temporary Boost paths")
- set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
- set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
- set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
- set(Boost_FOUND TRUE)
-endif()
-
-
message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}")
message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}")
message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}")
@@ -422,9 +331,9 @@
include(ExternalProject)
ExternalProject_Add(libcereal
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -o cereal-v1.2.2.tar.gz &&
- ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-v1.2.2.tar.gz &&
- tar -xzvf cereal-v1.2.2.tar.gz
+ DOWNLOAD_COMMAND cp ../../../distdir/cereal-1.2.2.tar.gz . &&
+ ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-1.2.2.tar.gz &&
+ tar -xzvf cereal-1.2.2.tar.gz
##
#URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz
@@ -455,12 +364,12 @@
ExternalProject_Add(libbwa
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
#URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz
- #DOWNLOAD_NAME bwa-master.tar.gz
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz &&
- ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 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
+ #DOWNLOAD_NAME bwa-0.7.12.5.tar.gz
+ DOWNLOAD_COMMAND cp ../../../distdir/bwa-0.7.12.5.tar.gz . &&
+ ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-0.7.12.5.tar.gz &&
+ mkdir -p bwa-0.7.12.5 &&
+ tar -xzvf bwa-0.7.12.5.tar.gz --strip-components=1 -C bwa-0.7.12.5
+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-0.7.12.5
INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
CONFIGURE_COMMAND ""
BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}"
@@ -562,9 +471,9 @@
message("==================================================================")
ExternalProject_Add(libgff
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz &&
- ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff.tgz &&
- tar -xzvf libgff.tgz
+ DOWNLOAD_COMMAND cp ../../../distdir/libgff-1.1.tgz . &&
+ ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff-1.1.tgz &&
+ tar -xzvf libgff-1.1.tgz
##
#URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
#DOWNLOAD_NAME libff.tgz
@@ -600,10 +509,10 @@
message("==================================================================")
ExternalProject_Add(libstadenio
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -o staden-io_lib-v1.14.8.tar.gz &&
- ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-v1.14.8.tar.gz &&
+ DOWNLOAD_COMMAND cp ../../../distdir/staden-io_lib-1.14.8.tar.gz . &&
+ ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-1.14.8.tar.gz &&
mkdir -p staden-io_lib-1.14.8 &&
- tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
+ tar -xzf staden-io_lib-1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
rm -fr staden-io_lib &&
mv -f staden-io_lib-1.14.8 staden-io_lib
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
@@ -620,9 +529,9 @@
message("==================================================================")
ExternalProject_Add(libspdlog
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz &&
- ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz &&
- tar -xzf spdlog-v0.16.1.tar.gz
+ DOWNLOAD_COMMAND cp ../../../distdir/spdlog-0.16.1.tar.gz . &&
+ ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-0.16.1.tar.gz &&
+ tar -xzf spdlog-0.16.1.tar.gz
##
#URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz
#DOWNLOAD_NAME spdlog-v0.12.0.tar.gz
|
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