Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 512136) +++ head/biology/Makefile (revision 512137) @@ -1,172 +1,173 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += consed SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm + SUBDIR += haplohseq SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster 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 += plinkseq SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-xenaPython 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 += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += wise .include Index: head/biology/haplohseq/Makefile =================================================================== --- head/biology/haplohseq/Makefile (nonexistent) +++ head/biology/haplohseq/Makefile (revision 512137) @@ -0,0 +1,29 @@ +# $FreeBSD$ + +PORTNAME= haplohseq +DISTVERSION= 0.1.2 +CATEGORIES= biology +MASTER_SITES= https://mirror1.hpc.uwm.edu/Distfiles/ \ + https://mirror2.hpc.uwm.edu/Distfiles/ +DISTNAME= haplohseq_source-${DISTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Identify regions of allelic imbalance + +LICENSE= MIT + +LIB_DEPENDS= libboost_system.so:devel/boost-libs + +USES= compiler:c++11-lang gmake localbase:ldflags zip + +MAKEFILE= makefile +WRKSRC= ${WRKDIR}/haplohseq_source +LDFLAGS+= -lpthread +MAKE_ENV= STRIP=${STRIP} + +PLIST_FILES= bin/haplohseq + +do-test: + @(cd ${WRKSRC}/build/test && ${FILESDIR}/run-tests) + +.include Property changes on: head/biology/haplohseq/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/haplohseq/distinfo =================================================================== --- head/biology/haplohseq/distinfo (nonexistent) +++ head/biology/haplohseq/distinfo (revision 512137) @@ -0,0 +1,3 @@ +TIMESTAMP = 1567118170 +SHA256 (haplohseq_source-0.1.2.zip) = 35f8fe6718020e6eacdc309d28fc5dd3cc7c6e8400da1d962fdf6fb52d4e90c5 +SIZE (haplohseq_source-0.1.2.zip) = 63620 Property changes on: head/biology/haplohseq/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/haplohseq/files/patch-makefile =================================================================== --- head/biology/haplohseq/files/patch-makefile (nonexistent) +++ head/biology/haplohseq/files/patch-makefile (revision 512137) @@ -0,0 +1,105 @@ +--- makefile.orig 2019-08-29 18:03:23 UTC ++++ makefile +@@ -7,23 +7,32 @@ + # + + # Constants +-CXX=g++ ++# Default to g++ if not set by make args or environment ++CXX?=g++ + #-O0 -g will turn on debugging + #The rule of thumb: + #When you need to debug, use -O0 (and -g to generate debugging symbols.) + #When you are preparing to ship it, use -O2. + #When you use gentoo, use -O3...! + #When you need to put it on an embedded system, use -Os (optimize for size, not for efficiency.) +-CXX_FLAGS=-Wall -g -stdlib=libstdc++ ++# Use canonincal compiler variables, which may be provided by build env ++CXXFLAGS?=-Wall -g -stdlib=libstdc++ + SRC=src + CONF=conf + HMM_SRC=$(SRC)/hmm + UTIL_SRC=$(SRC)/util +-BOOST=/usr/local/boost_1_52_0 ++BOOST?=/usr/local/boost_1_52_0 + INCLUDES=-I./$(SRC) -I./$(HMM_SRC) -I./$(UTIL_SRC) -isystem$(BOOST) +-LIBRARY_PATHS=-Llib/macosx ++LIBRARY_PATHS?=-Llib/macosx + LIBRARIES=-lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread + ++# Installation target with destdir support ++DESTDIR?=. ++PREFIX?=/usr/local ++MKDIR?=mkdir ++INSTALL?=install ++STRIP?= # empty, set to -s to install stripped binary ++ + # Generated directories which are generated in this script and cleaned up with 'make clean' + BUILD=build + OBJ=$(BUILD)/obj +@@ -35,18 +44,21 @@ directories: + + # Create object files into the OBJ directory from cpp files in the SRC directory. + $(OBJ)/%.o: $(SRC)/%.cpp directories +- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $< ++ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $< + $(OBJ)/%.o: $(HMM_SRC)/%.cpp directories +- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $< ++ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $< + $(OBJ)/%.o: $(UTIL_SRC)/%.cpp directories +- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $< ++ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $< + +-all: clean haplohseq ++all: haplohseq test + + haplohseq: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o +- $(CXX) -o $(BIN)/$@ $(CXX_FLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES) +- cp -r $(CONF) $(BIN)/. +- ++ $(CXX) -o $(BIN)/$@ $(CXXFLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) ++ ++install: ++ $(MKDIR) -p $(DESTDIR)$(PREFIX)/bin ++ $(INSTALL) -c $(STRIP) $(BIN)/* $(DESTDIR)$(PREFIX)/bin ++ + clean: + rm -rf $(BUILD) + +@@ -74,28 +86,28 @@ test: FreqPhaseTest HaplohSeqTest HmmTest InputProcess + + # Create test object files into the OBJ directory from cpp files in the SRC directory. + $(TEST_BIN)/%.o: $(TEST_SRC)/%.cpp directories test_directory +- $(CXX) $(CXX_FLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $< ++ $(CXX) $(CXXFLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $< + + HaplohSeqTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o +- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES) ++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) + + FreqPhaseTest: $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o +- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES) ++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) + + HmmTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o +- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES) ++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) + + InputProcessorTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o +- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES) ++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) + + MathUtilTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o +- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES) ++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) + + ReporterTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o +- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES) ++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) + + ThreadPoolTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o +- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES) ++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) + ############################## END TEST LOGIC ############################## + + Property changes on: head/biology/haplohseq/files/patch-makefile ___________________________________________________________________ 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/haplohseq/files/patch-src_HaplohSeq.cpp =================================================================== --- head/biology/haplohseq/files/patch-src_HaplohSeq.cpp (nonexistent) +++ head/biology/haplohseq/files/patch-src_HaplohSeq.cpp (revision 512137) @@ -0,0 +1,20 @@ +--- src/HaplohSeq.cpp.orig 2019-09-01 14:58:30 UTC ++++ src/HaplohSeq.cpp +@@ -202,7 +202,7 @@ void HaplohSeq::runBafHaplohseq( std::string& obsType, + + // Spawn worker threads + for (std::size_t t = 0; t < numThreads; t++) { +- threadPool.create_thread(boost::bind((unsigned long int (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ++ threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); + } + + std::map > chrHmms; +@@ -420,7 +420,7 @@ void HaplohSeq::runVcfHaplohseq( std::string& obsType, + + // Spawn worker threads + for (std::size_t t = 0; t < numThreads; t++) { +- threadPool.create_thread(boost::bind((unsigned long int (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ++ threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); + } + + std::map > chrHmms; Property changes on: head/biology/haplohseq/files/patch-src_HaplohSeq.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/haplohseq/files/patch-src_test_InputProcessorTest.cpp =================================================================== --- head/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp (nonexistent) +++ head/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp (revision 512137) @@ -0,0 +1,11 @@ +--- src/test/InputProcessorTest.cpp.orig 2019-09-01 12:33:22 UTC ++++ src/test/InputProcessorTest.cpp +@@ -82,7 +82,7 @@ BOOST_AUTO_TEST_CASE(isHetTest) { + BOOST_REQUIRE_EQUAL(inputProc.isHet('A','?'), false); + BOOST_REQUIRE_EQUAL(inputProc.isHet('A','.'), false); + BOOST_REQUIRE_EQUAL(inputProc.isHet('A',' '), false); +- BOOST_REQUIRE_EQUAL(inputProc.isHet('C', NULL), true); ++ BOOST_REQUIRE_EQUAL(inputProc.isHet('C','\0'), true); + } + + BOOST_AUTO_TEST_CASE(readAllelesTest) { Property changes on: head/biology/haplohseq/files/patch-src_test_InputProcessorTest.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/haplohseq/files/run-tests =================================================================== --- head/biology/haplohseq/files/run-tests (nonexistent) +++ head/biology/haplohseq/files/run-tests (revision 512137) @@ -0,0 +1,10 @@ +#!/bin/sh -e + +printf "\n=== FreqPhaseTest ===\n\n" +./FreqPhaseTest +printf "\n=== InputProcessorTest ===\n\n" +./InputProcessorTest +printf "\n=== HmmTest ===\n\n" +./HmmTest +printf "\n=== HaplohSeqTest ===\n\n" +./HaplohSeqTest Property changes on: head/biology/haplohseq/files/run-tests ___________________________________________________________________ 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/haplohseq/pkg-descr =================================================================== --- head/biology/haplohseq/pkg-descr (nonexistent) +++ head/biology/haplohseq/pkg-descr (revision 512137) @@ -0,0 +1,6 @@ +Haplohseq identifies regions of allelic imbalance (AI) in sequencing data +obtained from impure samples where AI events exist in a potentially low +proportion of cells in the sample. Input to the software includes a VCF file +of genotypes and estimated phased genotypes. + +WWW: https://sites.google.com/site/integrativecancergenomics/software/haplohseq Property changes on: head/biology/haplohseq/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