changes for final source release 1.2

packaging script CMake bug workaround for boost threads linking
fungs · Jul 7, 2014 · e1da430 · e1da430
1 parent 4203b15
commit e1da430
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Showing 3 changed files with 7 additions and 5 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -7,6 +7,7 @@ v. 1.2 taxator-tk (=SVN r61)
 * better approximation of identity scores + support values in binner
 * optimizations in RPA procedure
 * heuristic to avoid excessive run-time with bad alignments
+* workaround for CMake bug with boost threads linking
 
 v. 1.1 taxator-tk (=SVN r51)
 ============================

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -7,8 +7,9 @@ set( boost_version_required_enc 103401 )
 set( project_name taxator-tk )
 
 # cmake requirements detection
-set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake-modules)
-# find_package( Sqlite3 )
+set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake-modules ${CMAKE_MODULE_PATH})
+# find_package(Sqlite3)
+find_package(Threads REQUIRED)  # necessary workaround for cmake boost detection bug (not linking POSIX threads library)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_LIBS OFF)
 set(Boost_USE_STATIC_RUNTIME OFF)
@@ -42,7 +43,7 @@ target_link_libraries( alignments-filter ${Boost_PROGRAM_OPTIONS_LIBRARY} ${Boos
 # takes input alignments and predicts a taxon for each query id using various methods and parameters
 add_executable( taxator taxator.cpp src/taxontree.cpp src/taxonomyinterface.cpp src/ncbidata.cpp src/accessconv.cpp src/predictionrecord.cpp )
 #target_link_libraries( taxator boost_program_options boost_system boost_filesystem boost_thread )
-target_link_libraries( taxator ${Boost_PROGRAM_OPTIONS_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_FILESYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} )
+target_link_libraries( taxator ${Boost_PROGRAM_OPTIONS_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_FILESYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CMAKE_THREAD_LIBS_INIT} )
 
 # apply filtering to predictions file
 add_executable( binner binner.cpp src/taxontree.cpp src/taxonomyinterface.cpp src/ncbidata.cpp src/predictionrecord.cpp )

diff --git a/releasefiles.txt b/releasefiles.txt
@@ -15,14 +15,14 @@ acc2taxid.cpp
 alignments-filter.cpp
 binner.cpp
 extract-fastacomment-ncbifield.cpp
-name-filter.cpp
-rank-filter.cpp
 taxator.cpp
 unittest_ncbitaxonomy.cpp
+taxknife.cpp
 
 # taxator-tk classes and functions
 src/predictionrecord.hh
 src/fastnodemap.hh
+src/taxonfilter.hh
 src/taxonpredictionmodel.hh
 src/taxonpredictionmodelsequence.hh
 src/tree.hh