Commit d41fc64e authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.3.13+dfsg

parent a60f78b9

CMakeLists.txt

+11 −3
Original line number Diff line number Diff line
@@ -108,7 +108,7 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX) 
    if(${GCC_VERSION} VERSION_LESS 6.0)

      set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -std=gnu++14")

    else(${GCC_VERSION} VERSION_LESS 6.0)

      set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -std=c++14")

      set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3")

    endif(${GCC_VERSION} VERSION_LESS 6.0)



    if(NOAVX)
@@ -190,14 +190,22 @@ endif(NOT ${OPENMP_FOUND}) 
#-------------------------------------------------------------------------------

set(INSTALL_PREFIX /usr/local CACHE PATH "Installation prefix")

set(CMAKE_INSTALL_PREFIX ${INSTALL_PREFIX} CACHE INTERNAL "Installation prefix" FORCE)

if(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")

    set(DEFAULT_LIBRARIES pthread)

else(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")

    set(DEFAULT_LIBRARIES dl pthread)

endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")



#-------------------------------------------------------------------------------

# LIBCurl support

#-------------------------------------------------------------------------------

find_package(CURL)

if(${CURL_FOUND} AND NOT APPLE)

    if(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")

        set(DEFAULT_LIBRARIES pthread crypto curl ssl)

    else(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")

        set(DEFAULT_LIBRARIES dl pthread crypto curl ssl)

    endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")

    add_definitions (-D__HYPHYCURL__)

endif(${CURL_FOUND} AND NOT APPLE)

res/TemplateBatchFiles/BUSTED-SRV.bf

+1 −1
Original line number Diff line number Diff line 
RequireVersion ("2.1320141020");

RequireVersion ("2.13.20141020");



console.log("ERROR: THIS BATCHFILE WILL NOT RUN PROPERLY WITH UPDATED TERMS BASE. QUITTING.");

exit();

res/TemplateBatchFiles/BranchSiteREL.bf

+1 −1
Original line number Diff line number Diff line 
RequireVersion ("2.1320141101");

RequireVersion ("2.13.20141101");



_BSREL_timers  = {5,1};

taskTimerStart (4);

res/TemplateBatchFiles/DatedTipsMolecularClock.bf

+1 −1
Original line number Diff line number Diff line 
RequireVersion ("2.0020110101");

RequireVersion ("2.00.20110101");

VERBOSITY_LEVEL = -1;

res/TemplateBatchFiles/Gateaux.bf

+1 −1
Original line number Diff line number Diff line 
RequireVersion ("2.0020110101");

RequireVersion ("2.00.20110101");



ExecuteAFile  (HYPHY_LIB_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"TemplateModels"+DIRECTORY_SEPARATOR+"chooseGeneticCode.def");

ExecuteAFile  (HYPHY_LIB_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"2RatesAnalyses"+DIRECTORY_SEPARATOR+"MG94xREVxBivariate.mdl");