CMakeLists.txt

@@ -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)
 

debian/changelog

-hyphy (2.3.10+dfsg-1) UNRELEASED; urgency=medium
+hyphy (2.3.13+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
 
   [ Steffen Moeller ]
   * debian/upstream/metadata: Added ref to OMICtools
 
   [ Andreas Tille ]
   * New upstream version
-  * Standards-Version: 4.1.3
   * debhelper 11
   * Add Build-Depends: opencl-dev
+  * debian/rules:
+     - Do not parse d/changelog
+     - regard $(DEB_BUILD_OPTIONS) for override_dh_auto_test
 
   [ Liubov Chuprikova ]
   * Drop hyphygui as it was removed from upstream
   * Point Vcs fields to salsa.debian.org
   * Standards-Version: 4.1.5
 
- -- Andreas Tille <tille@debian.org>  Sun, 11 Feb 2018 10:45:54 +0100
+ -- Liubov Chuprikova <chuprikovalv@gmail.com>  Tue, 10 Jul 2018 08:39:13 +0200
 
 hyphy (2.2.7+dfsg-1) unstable; urgency=medium
 

debian/patches/debug_r_build.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Updated: Mon, 29 Jun 2015 11:13:57 +0200
-Description: Just for debugging, not activated
-
---- a/src/lib/build.sh
-+++ b/src/lib/build.sh
-@@ -72,6 +72,7 @@ fi
- 
- # END MODIFY
- 
-+set -x
- echo "Checking for curl";
- echo "#include <curl/curl.h>\nint main(void) {return 0;}" > curl_check.cpp
- 
-@@ -86,7 +87,7 @@ else
- fi
- 
- rm -rf curl_check*
--
-+set +x
- 	
- makedir () {
- 	if [ -f $1 ] 

debian/patches/drop_profiling_option.patch

@@ -5,7 +5,7 @@ Bug-Debian: http://bugs.debian.org/793345
 
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -408,8 +408,8 @@ add_custom_target(DEBUG DEPENDS HYPHYDEB
+@@ -416,8 +416,8 @@ add_custom_target(DEBUG DEPENDS HYPHYDEB
  set_target_properties(
      HYPHYDEBUG
      PROPERTIES
@@ -16,7 +16,7 @@ Bug-Debian: http://bugs.debian.org/793345
  )
  
  
-@@ -433,8 +433,8 @@ set_property(
+@@ -441,8 +441,8 @@ set_property(
  set_target_properties(
      HYPHYGTEST
      PROPERTIES

debian/patches/msse_option_only_if_available.patch

@@ -5,7 +5,7 @@ Last-Update: Thu, 23 Jul 2015 13:12:54 +0200
 
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -430,12 +430,23 @@ set_property(
+@@ -438,12 +438,23 @@ set_property(
      TARGET HYPHYGTEST
      APPEND PROPERTY COMPILE_DEFINITIONS __UNITTEST__
  )

debian/patches/spelling.patch

@@ -4,7 +4,7 @@ Description: Fix two spelling issues
 
 --- a/src/core/batchlan.cpp
 +++ b/src/core/batchlan.cpp
-@@ -7368,7 +7368,7 @@ bool    _ElementaryCommand::ConstructMPI
+@@ -7383,7 +7383,7 @@ bool    _ElementaryCommand::ConstructMPI
  
  //____________________________________________________________________________________
  bool    _ElementaryCommand::ConstructCategoryMatrix (_String&source, _ExecutionList&target)

debian/patches/use_debian_sqlite.patch

@@ -19,7 +19,7 @@ Description: Use Debian packaged sqlite3
  
  
  #-------------------------------------------------------------------------------
-@@ -202,6 +201,36 @@ if(${CURL_FOUND} AND NOT APPLE)
+@@ -210,6 +209,36 @@ if(${CURL_FOUND} AND NOT APPLE)
  endif(${CURL_FOUND} AND NOT APPLE)
  
  #-------------------------------------------------------------------------------
@@ -56,7 +56,7 @@ Description: Use Debian packaged sqlite3
  # gtest dependency
  #-------------------------------------------------------------------------------
  add_subdirectory(contrib/gtest-1.7.0)
-@@ -235,11 +264,6 @@ set_property(
+@@ -243,11 +272,6 @@ set_property(
  )
  
  set_property(
@@ -68,7 +68,7 @@ Description: Use Debian packaged sqlite3
      SOURCE src/core/calcnode2.cpp
      APPEND_STRING PROPERTY COMPILE_FLAGS " -fstrict-aliasing -funroll-loops"
  )
-@@ -261,7 +285,6 @@ endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
+@@ -269,7 +293,6 @@ endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
  include_directories(
      src/core/include
      src/lib/Link src/new/include

debian/rules

@@ -2,11 +2,11 @@
 
 # DH_VERBOSE := 1
 
-# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
 
-pkg=$(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-export PYBUILD_NAME=$(pkg)
+include /usr/share/dpkg/default.mk
+
+export PYBUILD_NAME=$(DEB_SOURCE)
 PYVERS = $(shell pyversions -r)
 PY3VERS = $(shell py3versions -r)
 
@@ -24,7 +24,9 @@ override_dh_auto_build:
 	dh_auto_build -- MP MPI GTEST # LIB
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	find obj-* -name HYPHYGTEST -exec \{\} \;
+endif
 
 override_dh_install:
 	# smallcaps for executables

res/TemplateBatchFiles/BUSTED-SRV.bf

-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

-RequireVersion ("2.1320141101");
+RequireVersion ("2.13.20141101");
 
 _BSREL_timers  = {5,1};
 taskTimerStart (4);

res/TemplateBatchFiles/DatedTipsMolecularClock.bf

-RequireVersion ("2.0020110101");
+RequireVersion ("2.00.20110101");
 VERBOSITY_LEVEL = -1;
 
 

res/TemplateBatchFiles/Gateaux.bf

-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");

res/TemplateBatchFiles/GateauxMR.bf

-RequireVersion ("0.9920060817");
+RequireVersion ("0.99.20060817");
 
 
 s_rateMin    = 0.01;

res/TemplateBatchFiles/LEISR.bf

@@ -32,7 +32,7 @@ leisr.analysis_description = {
     terms.io.info: "LEISR (Likelihood Estimation of Individual Site Rates) infer relative amino-acid or nucleotide rates from a fixed nucleotide or amino-acid alignment and tree, with possibility for partitions. Relative site-specific substitution rates are
     inferred by first optimizing alignment-wide branch lengths, and then inferring a site-specific uniform tree scaler.",
     terms.io.version: "0.4",
-    terms.io.reference: "Spielman, S.J. and Kosakovsky Pond, S.L. Relative evolutionary rate inference in HyPhy with LEISR. bioRxiv. https://doi.org/10.1101/206011. (2017); Pupko, T., Bell, R. E., Mayrose, I., Glaser, F. & Ben-Tal, N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18, S71–S77 (2002).",
+    terms.io.reference: "Spielman, S.J. and Kosakovsky Pond, S.L. (2018). Relative evolutionary rate inference in HyPhy with PeerJ 6:e4339. DOI 10.7717/peerj.4339 ; Pupko, T., Bell, R. E., Mayrose, I., Glaser, F. & Ben-Tal, N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18, S71–S77 (2002).",
     terms.io.authors: "Sergei L Kosakovsky Pond and Stephanie J Spielman",
     terms.io.contact: "{spond,stephanie.spielman}@temple.edu"
 };
@@ -145,6 +145,14 @@ leisr.alignment_wide_MLES = estimators.FitSingleModel_Ext (
                                                           None,
                                                           {terms.run_options.retain_lf_object: TRUE});
                                                           
+/* reconstruct ancestral states - */
+
+// SW20180516 - NOT YET SUPPORTED
+
+//leisr.ancestral_data = ancestral.build (leisr.alignment_wide_MLES[terms.likelihood_function], 0, FALSE);
+//console.log (leisr.ancestral_data);                                                   
+//return 0;
+
 ConstructCategoryMatrix (leisr.site_level_log_likelihoods, ^(leisr.alignment_wide_MLES[terms.likelihood_function]), SITE_LOG_LIKELIHOODS);
 DeleteObject (^(leisr.alignment_wide_MLES[terms.likelihood_function]));
 

res/TemplateBatchFiles/MEDS.bf

-RequireVersion ("2.0020101201");
+RequireVersion ("2.00.20101201");
 
 /*----------Branch-Site Directional Selection Analysis---------*/
 /*Usage: Takes an alignment and a tree (with foreground branches tagged with "{FG}"), a nucleotide model

res/TemplateBatchFiles/MEME_mf.bf

-RequireVersion  ("2.0020110101");
+RequireVersion  ("2.00.20110101");
 
 timer = Time(1);
 

res/TemplateBatchFiles/NucModelCompare.bf

-RequireVersion ("0.9920061127");
+RequireVersion ("0.99.20061127");
 
 /* 
 	This file takes a nucleotide data set and a tree (either from the data file or from a separate 	file) and computes maximum likelihood estimates for every possible 4x4 reversible model on that data and tree.

res/TemplateBatchFiles/Plato.bf

@@ -5,7 +5,7 @@
   October 2006
 */
 
-RequireVersion ("0.9920060901");
+RequireVersion ("0.99.20060901");
 
 VERBOSITY_LEVEL		  = -1; /* HELPS REDUCE GUI REFRESH OVERHEAD */
 ACCEPT_BRANCH_LENGTHS = 1;

res/TemplateBatchFiles/QuickSelectionDetectionMF.bf

-RequireVersion ("2.12");
+RequireVersion ("2.1.2");
 
 ExecuteAFile ("qndhelper1_mf.ibf");
 LoadFunctionLibrary ("GrabBag.bf");

res/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf

-RequireVersion ("2.1320141101");
+RequireVersion ("2.13.20141101");
 
 _BSREL_timers  = {5,1};
 taskTimerStart (4);