Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 468213) +++ head/biology/Makefile (revision 468214) @@ -1,137 +1,138 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += ddocent SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-macs2 SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += ssaha SUBDIR += stacks SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene + SUBDIR += unanimity SUBDIR += vcftools SUBDIR += vcflib SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/unanimity/Makefile =================================================================== --- head/biology/unanimity/Makefile (nonexistent) +++ head/biology/unanimity/Makefile (revision 468214) @@ -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 Property changes on: head/biology/unanimity/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ 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/distinfo =================================================================== --- head/biology/unanimity/distinfo (nonexistent) +++ head/biology/unanimity/distinfo (revision 468214) @@ -0,0 +1,3 @@ +TIMESTAMP = 1524324354 +SHA256 (PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz) = 20ed61c46afcfe86403a564136b96f909149208c51fde16f608e924ad4c59e38 +SIZE (PacificBiosciences-unanimity-g20180307-6f11a13e1472b8c00337ba8c5e94bf83bdab31d6_GH0.tar.gz) = 6492231 Property changes on: head/biology/unanimity/distinfo ___________________________________________________________________ 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-CMakeLists.txt =================================================================== --- head/biology/unanimity/files/patch-CMakeLists.txt (nonexistent) +++ head/biology/unanimity/files/patch-CMakeLists.txt (revision 468214) @@ -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 Property changes on: head/biology/unanimity/files/patch-CMakeLists.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-cmake_uny-config.cmake =================================================================== --- head/biology/unanimity/files/patch-cmake_uny-config.cmake (nonexistent) +++ head/biology/unanimity/files/patch-cmake_uny-config.cmake (revision 468214) @@ -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 "${UNY_RootDir}/CHANGELOG.md" UNANIMITY_CHANGELOG) + Property changes on: head/biology/unanimity/files/patch-cmake_uny-config.cmake ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake =================================================================== --- head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake (nonexistent) +++ head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake (revision 468214) @@ -0,0 +1,11 @@ +--- cmake/uny-gitsha1.cmake.orig 2018-03-07 23:10:34 UTC ++++ cmake/uny-gitsha1.cmake +@@ -7,7 +7,7 @@ set(__find_git_sha1 YES) + function(find_git_sha1 _GIT_SHA1) + find_package(Git QUIET REQUIRED) + execute_process(COMMAND +- "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=-dirty" ++ echo 6f11a13e1472b8c00337ba8c5e94bf83bdab31d6 + WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" + RESULT_VARIABLE res + OUTPUT_VARIABLE out Property changes on: head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake ___________________________________________________________________ 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-include_pacbio_genomicconsensus_Input.h =================================================================== --- head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Input.h (nonexistent) +++ head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Input.h (revision 468214) @@ -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; Property changes on: head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Input.h ___________________________________________________________________ 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-include_pacbio_genomicconsensus_Output.h =================================================================== --- head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Output.h (nonexistent) +++ head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Output.h (revision 468214) @@ -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) { Property changes on: head/biology/unanimity/files/patch-include_pacbio_genomicconsensus_Output.h ___________________________________________________________________ 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_CMakeLists.txt =================================================================== --- head/biology/unanimity/files/patch-src_CMakeLists.txt (nonexistent) +++ head/biology/unanimity/files/patch-src_CMakeLists.txt (revision 468214) @@ -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} Property changes on: head/biology/unanimity/files/patch-src_CMakeLists.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_Recursor.h =================================================================== --- head/biology/unanimity/files/patch-src_Recursor.h (nonexistent) +++ head/biology/unanimity/files/patch-src_Recursor.h (revision 468214) @@ -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::FillAlphaBeta( + size_t J = tpl.Length(); + int flipflops = 0; + size_t maxSize = +- std::max(100ul, static_cast(0.5 + REBANDING_THRESHOLD * (I + 1) * (J + 1))); ++ std::max(100ul, static_cast(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 Property changes on: head/biology/unanimity/files/patch-src_Recursor.h ___________________________________________________________________ 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-descr =================================================================== --- head/biology/unanimity/pkg-descr (nonexistent) +++ head/biology/unanimity/pkg-descr (revision 468214) @@ -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 Property changes on: head/biology/unanimity/pkg-descr ___________________________________________________________________ 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