Index: head/biology/unanimity/Makefile =================================================================== --- head/biology/unanimity/Makefile (revision 493401) +++ head/biology/unanimity/Makefile (revision 493402) @@ -1,43 +1,43 @@ # $FreeBSD$ PORTNAME= unanimity DISTVERSIONPREFIX= v -DISTVERSION= 3.1.0 -PORTREVISION= 2 +DISTVERSION= 3.4.0 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Pacific Biosciences consensus library and applications LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_aarch64= fails to compile: mmintrin.h:47:5: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'? -# Sensitive to dependency versions, use latest commit for everything -BUILD_DEPENDS= pbseqan>=g20171002:biology/pbseqan \ - pbbam>=g20180416:biology/pbbam \ - pbcopper>=g20180413:biology/pbcopper +# Very sensitive to pbbam and pbcopper versions! +# Fully test new combinations and upgrade them together. +BUILD_DEPENDS= seqan>=2.4.0:biology/seqan \ + swig30>=3.0:devel/swig30 \ + ${PYNUMPY} LIB_DEPENDS= libhts.so:biology/htslib \ - libboost_regex.so:devel/boost-libs + libboost_regex.so:devel/boost-libs \ + libpbbam.so.0.18.0:biology/pbbam \ + libpbcopper.so.0.4.1:biology/pbcopper +RUN_DEPENDS= ${PYNUMPY} -USES= cmake:insource compiler:c++14-lang pkgconfig python +# Meson needs BOOST_ROOT=${LOCALBASE} +# https://github.com/mesonbuild/meson/issues/2239 +USES= compiler:c++14-lang localbase meson pkgconfig python +USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= PacificBiosciences -CMAKE_ARGS+= -DHTSLIB_INCLUDE_DIRS:STRING=${LOCALBASE}/include/htslib \ - -DHTSLIB_LIBRARIES:STRING="-L${LOCALBASE}/lib -lhts" \ - -DPacBioBAM_INCLUDE_DIRS:STRING=${LOCALBASE}/include/pbbam \ - -DPacBioBAM_LIBRARIES:STRING="-L${LOCALBASE}/lib -lpbbam" \ - -DSEQAN_INCLUDE_DIRS:STRING=${LOCALBASE}/include/PacBio \ - -Dpbcopper_INCLUDE_DIRS=${LOCALBASE}/include \ - -Dpbcopper_LIBRARIES="-L${LOCALBASE}/lib -lpbcopper" CFLAGS_i386= -msse2 -Wno-c++11-narrowing +LDFLAGS+= -lexecinfo -PLIST_FILES= bin/arrow bin/ccs bin/gcpp lib/libcc2.a lib/libunanimity.a - post-install: - ${INSTALL_DATA} ${WRKSRC}/src/libcc2.a ${WRKSRC}/src/libunanimity.a \ - ${STAGEDIR}${PREFIX}/lib + ${RLN} ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0.0 \ + ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0 + ${RLN} ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0.0 \ + ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3 .include Index: head/biology/unanimity/distinfo =================================================================== --- head/biology/unanimity/distinfo (revision 493401) +++ head/biology/unanimity/distinfo (revision 493402) @@ -1,3 +1,3 @@ -TIMESTAMP = 1534907295 -SHA256 (PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz) = 355866bd3f83bf1f7c322269c01d3c2f943e30942455741d6e802b0ad3f89912 -SIZE (PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz) = 6493202 +TIMESTAMP = 1550617512 +SHA256 (PacificBiosciences-unanimity-v3.4.0_GH0.tar.gz) = cb2fd361b2cae1196e710e4d0b8af3b03a7f09145f96ce8aa7d2aef2401ca8e0 +SIZE (PacificBiosciences-unanimity-v3.4.0_GH0.tar.gz) = 6493566 Index: head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake =================================================================== --- head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake (revision 493401) +++ head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake (nonexistent) @@ -1,11 +0,0 @@ ---- cmake/uny-gitsha1.cmake.orig 2018-03-07 23:10:34 UTC -+++ cmake/uny-gitsha1.cmake -@@ -7,7 +7,7 @@ set(__find_git_sha1 YES) - function(find_git_sha1 _GIT_SHA1) - find_package(Git QUIET REQUIRED) - execute_process(COMMAND -- "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=-dirty" -+ echo 6f11a13e1472b8c00337ba8c5e94bf83bdab31d6 - WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" - RESULT_VARIABLE res - OUTPUT_VARIABLE out Property changes on: head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/unanimity/files/patch-CMakeLists.txt =================================================================== --- head/biology/unanimity/files/patch-CMakeLists.txt (revision 493401) +++ head/biology/unanimity/files/patch-CMakeLists.txt (nonexistent) @@ -1,11 +0,0 @@ ---- CMakeLists.txt.orig 2018-03-07 23:10:34 UTC -+++ CMakeLists.txt -@@ -37,7 +37,7 @@ include(uny-ccache) - include(uny-releasewithassert) - include(uny-dependencies) - include(uny-compilerflags) --include(uny-gitsha1) -+# include(uny-gitsha1) - include(uny-config) - - # Build library Property changes on: head/biology/unanimity/files/patch-CMakeLists.txt ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/unanimity/files/patch-cmake_uny-config.cmake =================================================================== --- head/biology/unanimity/files/patch-cmake_uny-config.cmake (revision 493401) +++ head/biology/unanimity/files/patch-cmake_uny-config.cmake (nonexistent) @@ -1,10 +0,0 @@ ---- cmake/uny-config.cmake.orig 2016-09-12 19:55:43 UTC -+++ cmake/uny-config.cmake -@@ -1,6 +1,6 @@ - # Config generation - --find_git_sha1(UNANIMITY_GIT_SHA1) -+# find_git_sha1(UNANIMITY_GIT_SHA1) - - file (STRINGS "${UNY_RootDir}/CHANGELOG.md" UNANIMITY_CHANGELOG) - Property changes on: head/biology/unanimity/files/patch-cmake_uny-config.cmake ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/unanimity/files/patch-src_CMakeLists.txt =================================================================== --- head/biology/unanimity/files/patch-src_CMakeLists.txt (revision 493401) +++ head/biology/unanimity/files/patch-src_CMakeLists.txt (nonexistent) @@ -1,15 +0,0 @@ ---- src/CMakeLists.txt.orig 2018-03-07 23:10:34 UTC -+++ src/CMakeLists.txt -@@ -53,11 +53,11 @@ configure_file( - - # includes - set(UNY_INCLUDE_DIRS -+ ${SEQAN_INCLUDE_DIRS} - ${UNY_IncludeDir} - ${CMAKE_BINARY_DIR}/generated - ${Boost_INCLUDE_DIRS} - ${HTSLIB_INCLUDE_DIRS} -- ${SEQAN_INCLUDE_DIRS} - ${CPPOPTPARSE_IncludeDir} - ${PacBioBAM_INCLUDE_DIRS} - ${pbcopper_INCLUDE_DIRS} Property changes on: head/biology/unanimity/files/patch-src_CMakeLists.txt ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/unanimity/files/patch-meson.build =================================================================== --- head/biology/unanimity/files/patch-meson.build (nonexistent) +++ head/biology/unanimity/files/patch-meson.build (revision 493402) @@ -0,0 +1,11 @@ +--- meson.build.orig 2019-02-17 22:59:57 UTC ++++ meson.build +@@ -90,7 +90,7 @@ subdir('src') + + if (not meson.is_subproject()) and get_option('swig') + uny_python_interp = find_program(get_option('PYTHON'), required : true) +- uny_swig = find_program('swig', required : true) ++ uny_swig = find_program('swig3.0', required : true) + + uny_pv_ver = run_command(uny_python_interp, ['-c', 'import sys; sys.stdout.write(sys.version[:3])']).stdout() + message('Python version: ' + uny_pv_ver) Property changes on: head/biology/unanimity/files/patch-meson.build ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/unanimity/files/patch-meson__options.txt =================================================================== --- head/biology/unanimity/files/patch-meson__options.txt (nonexistent) +++ head/biology/unanimity/files/patch-meson__options.txt (revision 493402) @@ -0,0 +1,8 @@ +--- meson_options.txt.orig 2019-02-17 22:53:47 UTC ++++ meson_options.txt +@@ -1,4 +1,4 @@ +-option('tests', type : 'boolean', value : true, description : 'Enable dependencies required for testing') ++option('tests', type : 'boolean', value : false, description : 'Enable dependencies required for testing') + + # python: + option('swig', type : 'boolean', value : true, description : 'Build UNANMITIY\'s SWIG interfacing code') Property changes on: head/biology/unanimity/files/patch-meson__options.txt ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp =================================================================== --- head/biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp (nonexistent) +++ head/biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp (revision 493402) @@ -0,0 +1,9 @@ +--- src/variantCaller/variantCaller.cpp.orig 2019-02-17 23:15:10 UTC ++++ src/variantCaller/variantCaller.cpp +@@ -1,5 +1,6 @@ + // Author: David Seifert + ++#include + #include + #include + Property changes on: head/biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/unanimity/pkg-plist =================================================================== --- head/biology/unanimity/pkg-plist (nonexistent) +++ head/biology/unanimity/pkg-plist (revision 493402) @@ -0,0 +1,82 @@ +bin/ChimeraLabeler +bin/arrow +bin/ccs +bin/ccs_sim +bin/gcpp +bin/genomic_sim +bin/variantCaller +include/pacbio/UnanimityConfig.h +include/pacbio/UnanimityVersion.h +include/pacbio/align/AffineAlignment.h +include/pacbio/align/AlignConfig.h +include/pacbio/align/BandedAligner.h +include/pacbio/align/BandedChainAlignment.h +include/pacbio/align/ChainScorer.h +include/pacbio/align/ChainSeeds.h +include/pacbio/align/ChainSeedsConfig.h +include/pacbio/align/FilterSeeds.h +include/pacbio/align/FindSeeds.h +include/pacbio/align/FindSeedsConfig.h +include/pacbio/align/HomopolymerHasher.h +include/pacbio/align/LinearAlignment.h +include/pacbio/align/LocalAlignment.h +include/pacbio/align/PairwiseAlignment.h +include/pacbio/align/SeedScorer.h +include/pacbio/align/SparseAlignment.h +include/pacbio/align/internal/BCAlignBlocks.h +include/pacbio/align/internal/BCAlignImpl.h +include/pacbio/ccs/Consensus.h +include/pacbio/ccs/ConsensusSettings.h +include/pacbio/ccs/SparseAlignment.h +include/pacbio/ccs/Whitelist.h +include/pacbio/chimera/ChimeraLabel.h +include/pacbio/chimera/ChimeraLabeler.h +include/pacbio/chimera/ChimeraResultWriter.h +include/pacbio/consensus/AbstractMatrix.h +include/pacbio/consensus/Coverage.h +include/pacbio/consensus/EasyReadScorer.h +include/pacbio/consensus/Evaluator.h +include/pacbio/consensus/Integrator.h +include/pacbio/consensus/IntervalMask.h +include/pacbio/consensus/MatrixViewConvention.h +include/pacbio/consensus/ModelConfig.h +include/pacbio/consensus/ModelSelection.h +include/pacbio/consensus/Mutation.h +include/pacbio/consensus/Polish.h +include/pacbio/consensus/PolishResult.h +include/pacbio/consensus/Template.h +include/pacbio/consensus/internal/ModelInternalInitializer.h +include/pacbio/data/ChemistryMapping.h +include/pacbio/data/ChemistryTriple.h +include/pacbio/data/Interval.h +include/pacbio/data/IntervalTree.h +include/pacbio/data/PlainOption.h +include/pacbio/data/Read.h +include/pacbio/data/ReadId.h +include/pacbio/data/Sequence.h +include/pacbio/data/State.h +include/pacbio/data/StrandType.h +include/pacbio/data/SubreadResultCounter.h +include/pacbio/data/internal/BaseEncoding.h +include/pacbio/data/internal/ConversionFunctions.h +include/pacbio/denovo/PoaConsensus.h +include/pacbio/denovo/PoaGraph.h +include/pacbio/denovo/RangeFinder.h +include/pacbio/denovo/SparsePoa.h +include/pacbio/exception/CCSExceptions.h +include/pacbio/exception/InvalidEvaluatorException.h +include/pacbio/exception/ModelError.h +include/pacbio/exception/StateError.h +include/pacbio/io/Utility.h +include/pacbio/parallel/WorkQueue.h +include/pacbio/util/ExecUtils.h +include/pacbio/util/Timer.h +lib/libunanimity.so +lib/libunanimity.so.3 +lib/libunanimity.so.3.0 +lib/libunanimity.so.3.0.0 +%%PYTHON_SITELIBDIR%%/ConsensusCore2.py +%%PYTHON_SITELIBDIR%%/ConsensusCore2.pyc +%%PYTHON_SITELIBDIR%%/ConsensusCore2.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/_ConsensusCore2.so +libdata/pkgconfig/unanimity.pc Property changes on: head/biology/unanimity/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property