Author: Michael R. Crusoe <crusoe@ucdavis.edu>
Description: Use Debian version of dependencies, don't download them
--- salmon.orig/CMakeLists.txt
+++ salmon/CMakeLists.txt
@@ -22,7 +22,7 @@
 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 
@@ -165,7 +165,7 @@
 ##
 # We want static, multithreaded boost libraries
 ##
-set (Boost_USE_STATIC_LIBS ON)
+set (Boost_USE_STATIC_LIBS OFF)
 set (Boost_USE_MULTITHREADED ON)
 #set (Boost_USE_STATIC_RUNTIME OFF)
 
@@ -322,51 +322,53 @@
 	
 set(EXTERNAL_LIBRARY_PATH $CMAKE_CURRENT_SOURCE_DIR/lib)
 
-message("Build system will fetch and build the Cereal serialization library")
-message("==================================================================")
-include(ExternalProject)
-ExternalProject_Add(libcereal
-    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-    URL http://www.cs.cmu.edu/~robp/files/cereal-v1.0.0.tgz
-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.0.0
-    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-1.0.0/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
-)
-
-message("Build system will fetch and build Jellyfish")
-message("==================================================================")
-ExternalProject_Add(libjellyfish
-    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-    URL ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3
-    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-    CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3/configure --prefix=<INSTALL_DIR> CC=${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 && 
-                    cp config.h <INSTALL_DIR>/include/jellyfish-2.1.3/jellyfish/ &&
-                    cp config.h <INSTALL_DIR>/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
+#    URL http://www.cs.cmu.edu/~robp/files/cereal-v1.0.0.tgz
+#    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.0.0
+#    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-1.0.0/build
+#    CONFIGURE_COMMAND ""
+#    BUILD_COMMAND ""
+#    INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/include && cp -r <SOURCE_DIR>/include/cereal <INSTALL_DIR>/include"
+#)
+
+#find_package(bwa)
+
+#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
+#)
+
+#message("Build system will fetch and build Jellyfish")
+#message("==================================================================")
+#ExternalProject_Add(libjellyfish
+#    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+#    URL ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
+#    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3
+#    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+#    CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3/configure --prefix=<INSTALL_DIR> CC=${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 && 
+#                    cp config.h <INSTALL_DIR>/include/jellyfish-2.1.3/jellyfish/ &&
+#                    cp config.h <INSTALL_DIR>/include/
+#)
 
 find_package(TBB)
 
@@ -375,124 +377,124 @@
 # 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()
+#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/tbb43_20140724oss)
+#set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
 
-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/tbb43_20140724oss)
-set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
-
-if ("${TBB_COMPILER}" STREQUAL "gcc") 
+#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 http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz
-    DOWNLOAD_COMMAND curl -k -L  http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz -o tbb_20140724oss_src.tgz &&
-                     tar -xzvf tbb_20140724oss_src.tgz
-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
-    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/* ${TBB_INSTALL_DIR}/include"
-    BUILD_IN_SOURCE 1
-)
+    #    set(TBB_CXXFLAGS "${TBB_CXXFLAGS} -UDO_ITT_NOTIFY")  
+#endif()
 
-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()
+#ExternalProject_Add(libtbb
+#	DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+#    URL http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz
+#    DOWNLOAD_COMMAND curl -k -L  http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz -o tbb_20140724oss_src.tgz &&
+#                     tar -xzvf tbb_20140724oss_src.tgz
+#    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
+#    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
-    URL http://www.cs.cmu.edu/~robp/files/libgff.tgz
-    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 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}
-    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/v1.5.tar.gz -o spdlog-v1.5.tar.gz &&
-                     tar -xzf spdlog-v1.5.tar.gz &&
-                     rm -fr spdlog &&
-                     mv -f  spdlog-1.5 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 libgff")
+#message("==================================================================")
+#ExternalProject_Add(libgff
+#    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+#    URL http://www.cs.cmu.edu/~robp/files/libgff.tgz
+#    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 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}
+#    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/v1.5.tar.gz -o spdlog-v1.5.tar.gz &&
+#                     tar -xzf spdlog-v1.5.tar.gz &&
+#                     rm -fr spdlog &&
+#                     mv -f  spdlog-1.5 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)
@@ -516,23 +518,23 @@
     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/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz &&
-        tar -xzf jemalloc-3.6.0.tar.gz 
-        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-3.6.0
-        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/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz &&
+#        tar -xzf jemalloc-3.6.0.tar.gz 
+#        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-3.6.0
+#        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 ()
 
 ###
 #
--- salmon.orig/src/CMakeLists.txt
+++ salmon/src/CMakeLists.txt
@@ -38,12 +38,8 @@
 
 include_directories( 
 ${GAT_SOURCE_DIR}/include
-${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-2.1.3
-${GAT_SOURCE_DIR}/external/install/include/bwa
+/usr/include/eigen3
+/usr/include/bwa
 ${ZLIB_INCLUDE_DIR}
 ${TBB_INCLUDE_DIRS}
 ${Boost_INCLUDE_DIRS}
@@ -74,7 +70,7 @@
 set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
 
 # Build the Salmon library
-add_library(salmon_core STATIC ${SALMON_LIB_SRCS} )
+add_library(salmon_core ${SALMON_LIB_SRCS} )
 
 # Build the salmon executable
 add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
@@ -107,10 +103,10 @@
     gff
     ${PTHREAD_LIB}
     ${Boost_LIBRARIES} 
-    ${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a
+    libstaden-read.so
     ${ZLIB_LIBRARY} 
-    ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a 
-    ${GAT_SOURCE_DIR}/external/install/lib/libbwa.a
+    libjellyfish-2.0.so 
+    /usr/lib/libbwa.a
     m
     ${LIBLZMA_LIBRARIES}
     ${BZIP2_LIBRARIES}
