Date: Tue, 24 Apr 2018 14:16:46 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r468214 - in head/biology: . unanimity unanimity/files Message-ID: <201804241416.w3OEGkDJ042527@repo.freebsd.org>
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Author: jwb Date: Tue Apr 24 14:16:46 2018 New Revision: 468214 URL: https://svnweb.freebsd.org/changeset/ports/468214 Log: biology/unanimity: Pacific Biosciences consensus library and applications Reviewed by: jrm Differential Revision: https://reviews.freebsd.org/D15172 Added: head/biology/unanimity/ head/biology/unanimity/Makefile (contents, props changed) head/biology/unanimity/distinfo (contents, props changed) head/biology/unanimity/files/ head/biology/unanimity/files/patch-CMakeLists.txt (contents, props changed) head/biology/unanimity/files/patch-cmake_uny-config.cmake (contents, props changed) head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake (contents, props changed) head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Input.h (contents, props changed) head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Output.h (contents, props changed) head/biology/unanimity/files/patch-src_CMakeLists.txt (contents, props changed) head/biology/unanimity/files/patch-src_Recursor.h (contents, props changed) head/biology/unanimity/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Tue Apr 24 14:06:34 2018 (r468213) +++ head/biology/Makefile Tue Apr 24 14:16:46 2018 (r468214) @@ -128,6 +128,7 @@ SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene + SUBDIR += unanimity SUBDIR += vcftools SUBDIR += vcflib SUBDIR += velvet Added: head/biology/unanimity/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/Makefile Tue Apr 24 14:16:46 2018 (r468214) @@ -0,0 +1,40 @@ +# $FreeBSD$ + +PORTNAME= unanimity +DISTVERSION= g20180307 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Pacific Biosciences consensus library and applications + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +# Sensitive to dependency versions, use latest commit for everything +BUILD_DEPENDS= pbseqan==g20171002:biology/pbseqan \ + pbbam==g20180416:biology/pbbam \ + pbcopper==g20180413:biology/pbcopper +LIB_DEPENDS= libhts.so:biology/htslib \ + libboost_regex.so:devel/boost-libs + +USES= cmake pkgconfig python +USE_GITHUB= yes +GH_ACCOUNT= PacificBiosciences +GH_TAGNAME= 6f11a13e1472b8c00337ba8c5e94bf83bdab31d6 + +CMAKE_ARGS+= -DHTSLIB_INCLUDE_DIRS:STRING=${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 + +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 + +.include <bsd.port.mk> Added: head/biology/unanimity/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/distinfo Tue Apr 24 14:16:46 2018 (r468214) @@ -0,0 +1,3 @@ +TIMESTAMP = 1524324354 +SHA256 (PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz) = 20ed61c46afcfe86403a564136b96f909149208c51fde16f608e924ad4c59e38 +SIZE (PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz) = 6492231 Added: head/biology/unanimity/files/patch-CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/files/patch-CMakeLists.txt Tue Apr 24 14:16:46 2018 (r468214) @@ -0,0 +1,11 @@ +--- 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 Added: head/biology/unanimity/files/patch-cmake_uny-config.cmake ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/files/patch-cmake_uny-config.cmake Tue Apr 24 14:16:46 2018 (r468214) @@ -0,0 +1,10 @@ +--- 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 "${UNY_RootDir}/CHANGELOG.md" UNANIMITY_CHANGELOG) + Added: head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake Tue Apr 24 14:16:46 2018 (r468214) @@ -0,0 +1,11 @@ +--- cmake/uny-gitsha1.cmake.orig 2018-03-07 23:10:34 UTC ++++ cmake/uny-gitsha1.cmake +@@ -7,7 +7,7 @@ set(__find_git_sha1 YES) + function(find_git_sha1 _GIT_SHA1) + find_package(Git QUIET REQUIRED) + execute_process(COMMAND +- "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=-dirty" ++ echo 6f11a13e1472b8c00337ba8c5e94bf83bdab31d6 + WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" + RESULT_VARIABLE res + OUTPUT_VARIABLE out Added: head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Input.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Input.h Tue Apr 24 14:16:46 2018 (r468214) @@ -0,0 +1,16 @@ +--- include/pacbio/genomicconsensus/Input.h.orig 2018-03-07 23:10:34 UTC ++++ include/pacbio/genomicconsensus/Input.h +@@ -25,7 +25,12 @@ namespace GenomicConsensus { + class Input + { + public: +- explicit Input(const Settings& settings) : settings_{settings} {} ++ // Original ++ //explicit Input(const Settings& settings) : settings_{settings} {} ++ // Probably OK ++ //explicit Input(const Settings& settings) { settings_ = settings; } ++ // https://forums.freebsd.org/threads/compile-error-with-clang-3-4.65595/#post-385293 ++ explicit Input(const Settings& settings) : settings_(settings) {} + + Input() = delete; + Input(const Input&) = delete; Added: head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Output.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Output.h Tue Apr 24 14:16:46 2018 (r468214) @@ -0,0 +1,19 @@ +--- include/pacbio/genomicconsensus/Output.h.orig 2018-03-07 23:10:34 UTC ++++ include/pacbio/genomicconsensus/Output.h +@@ -80,8 +80,15 @@ inline void PrintVcfLite(const Variant& + << "\tPASS\n"; + } + +-inline Output::Output(const Settings& settings) : settings_{settings} ++// Original ++//inline Output::Output(const Settings& settings) : settings_{settings} ++// Probably OK patch ++//inline Output::Output(const Settings& settings) ++// https://forums.freebsd.org/threads/compile-error-with-clang-3-4.65595/#post-385293 ++inline Output::Output(const Settings& settings) : settings_(settings) + { ++ // Probably OK patch ++ //settings_ = settings; + // initialize maps + PacBio::BAM::FastaSequenceQuery fasta{settings_.referenceFilename}; + for (const auto& seq : fasta) { Added: head/biology/unanimity/files/patch-src_CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/files/patch-src_CMakeLists.txt Tue Apr 24 14:16:46 2018 (r468214) @@ -0,0 +1,15 @@ +--- 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} Added: head/biology/unanimity/files/patch-src_Recursor.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/files/patch-src_Recursor.h Tue Apr 24 14:16:46 2018 (r468214) @@ -0,0 +1,12 @@ +# Type mismatch on 11.0 i386 +--- src/Recursor.h.orig 2018-03-07 23:10:34 UTC ++++ src/Recursor.h +@@ -708,7 +708,7 @@ size_t Recursor<Derived>::FillAlphaBeta( + size_t J = tpl.Length(); + int flipflops = 0; + size_t maxSize = +- std::max(100ul, static_cast<size_t>(0.5 + REBANDING_THRESHOLD * (I + 1) * (J + 1))); ++ std::max(100ul, static_cast<unsigned long>(0.5 + REBANDING_THRESHOLD * (I + 1) * (J + 1))); + + // if we use too much space, do at least one more round + // to take advantage of rebanding Added: head/biology/unanimity/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/pkg-descr Tue Apr 24 14:16:46 2018 (r468214) @@ -0,0 +1,8 @@ +Unanimity is a C++ library + applications to generate and process accurate +consensus sequences from Pacific Biosciences sequence data. + +The core binary, CCS (circular consensus calling) takes multiple reads of the +same SMRTbell sequence and combines them, employing a statistical model, to +produce one high quality consensus sequence. + +WWW: https://github.com/PacificBiosciences/unanimity
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