diff options
Diffstat (limited to 'biology')
32 files changed, 347 insertions, 67 deletions
diff --git a/biology/Makefile b/biology/Makefile index c7fbca643048..5e5cd3313b57 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -51,6 +51,7 @@ SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm + SUBDIR += haplohseq SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer @@ -127,6 +128,7 @@ SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 + SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx diff --git a/biology/abyss/Makefile b/biology/abyss/Makefile index 55eb657e2ca4..bf9b3195d646 100644 --- a/biology/abyss/Makefile +++ b/biology/abyss/Makefile @@ -2,7 +2,7 @@ PORTNAME= abyss DISTVERSION= 2.1.5 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= biology MASTER_SITES= http://www.bcgsc.ca/platform/bioinfo/software/${PORTNAME}/releases/${DISTVERSION}/ diff --git a/biology/chemeq/Makefile b/biology/chemeq/Makefile index 984c3ca48b3d..09cd7a92e693 100644 --- a/biology/chemeq/Makefile +++ b/biology/chemeq/Makefile @@ -16,6 +16,8 @@ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN= unfetchable +DEPRECATED= Unfetchable, unmaintained +EXPIRATION_DATE= 2019-10-16 MAKE_ARGS= CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" WRKSRC= ${WRKDIR}/${PORTNAME}-1.5 diff --git a/biology/diamond/Makefile b/biology/diamond/Makefile index 7ad594e8c8df..62003950ca42 100644 --- a/biology/diamond/Makefile +++ b/biology/diamond/Makefile @@ -2,7 +2,7 @@ PORTNAME= diamond DISTVERSIONPREFIX= v -DISTVERSION= 0.9.25 +DISTVERSION= 0.9.26 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org diff --git a/biology/diamond/distinfo b/biology/diamond/distinfo index 41d15c34274c..4ce87408bead 100644 --- a/biology/diamond/distinfo +++ b/biology/diamond/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1564956270 -SHA256 (bbuchfink-diamond-v0.9.25_GH0.tar.gz) = 65298f60cf9421dcc7669ce61642611cd9eeffc32f66fd39ebfa25dd64416808 -SIZE (bbuchfink-diamond-v0.9.25_GH0.tar.gz) = 406809 +TIMESTAMP = 1568831490 +SHA256 (bbuchfink-diamond-v0.9.26_GH0.tar.gz) = 09f9ef48ffe25ae5627ba4511e94be3a2573cfc45b0d813b9698916ff7db7f9b +SIZE (bbuchfink-diamond-v0.9.26_GH0.tar.gz) = 410524 diff --git a/biology/fastqc/Makefile b/biology/fastqc/Makefile index 49fcd206356c..6e837ffd263e 100644 --- a/biology/fastqc/Makefile +++ b/biology/fastqc/Makefile @@ -1,11 +1,10 @@ # $FreeBSD$ PORTNAME= fastqc -DISTVERSIONPREFIX= v -DISTVERSION= 0.11.5 +DISTVERSION= 0.11.8 CATEGORIES= biology java perl5 MASTER_SITES= https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ -DISTNAME= ${PORTNAME}_${DISTVERSIONPREFIX}${DISTVERSION} +DISTNAME= ${PORTNAME}_v${DISTVERSIONPREFIX}${DISTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Quality control tool for high throughput sequence data @@ -13,14 +12,14 @@ COMMENT= Quality control tool for high throughput sequence data LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.txt -NO_ARCH= yes -NO_BUILD= yes - USES= zip perl5 shebangfix -SHEBANG_FILES= fastqc USE_JAVA= yes USE_PERL5= run +SHEBANG_FILES= fastqc + +NO_ARCH= yes +NO_BUILD= yes WRKSRC= ${WRKDIR}/FastQC post-patch: @@ -31,10 +30,9 @@ post-patch: # Help files are not optional docs, but required for Help menu functionality do-install: - ${MKDIR} ${STAGEDIR}${JAVAJARDIR}/fastqc + @${MKDIR} ${STAGEDIR}${JAVAJARDIR}/fastqc ${INSTALL_DATA} ${WRKSRC}/*.jar ${STAGEDIR}${JAVAJARDIR}/fastqc - ${INSTALL_SCRIPT} ${WRKSRC}/fastqc \ - ${STAGEDIR}${PREFIX}/bin + ${INSTALL_SCRIPT} ${WRKSRC}/fastqc ${STAGEDIR}${PREFIX}/bin cd ${WRKSRC} && ${COPYTREE_SHARE} "Configuration Help Templates" \ ${STAGEDIR}${DATADIR} cd ${WRKSRC} && ${COPYTREE_SHARE} "net org uk" \ diff --git a/biology/fastqc/distinfo b/biology/fastqc/distinfo index df179e654f3f..6c217f90719c 100644 --- a/biology/fastqc/distinfo +++ b/biology/fastqc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1509737655 -SHA256 (fastqc_v0.11.5.zip) = dd7a5ad80ceed2588cf6d6ffe35e0f161c0d9977ed08355f5e4d9473282cbd66 -SIZE (fastqc_v0.11.5.zip) = 10026429 +TIMESTAMP = 1538750959 +SHA256 (fastqc_v0.11.8.zip) = ca87fe77807e4ac796b6cad949858921fd20652c4038f586f05ece94b5022129 +SIZE (fastqc_v0.11.8.zip) = 10255059 diff --git a/biology/fastqc/pkg-descr b/biology/fastqc/pkg-descr index 4ee7f74214dd..d8cfc6cb88bc 100644 --- a/biology/fastqc/pkg-descr +++ b/biology/fastqc/pkg-descr @@ -2,6 +2,6 @@ FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any -further analysis. +further analysis. WWW: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ diff --git a/biology/haplohseq/Makefile b/biology/haplohseq/Makefile new file mode 100644 index 000000000000..910cac75d6cb --- /dev/null +++ b/biology/haplohseq/Makefile @@ -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 && ${FILESDIR}/run-tests) + +.include <bsd.port.mk> diff --git a/biology/haplohseq/distinfo b/biology/haplohseq/distinfo new file mode 100644 index 000000000000..b5acbd168de0 --- /dev/null +++ b/biology/haplohseq/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1567118170 +SHA256 (haplohseq_source-0.1.2.zip) = 35f8fe6718020e6eacdc309d28fc5dd3cc7c6e8400da1d962fdf6fb52d4e90c5 +SIZE (haplohseq_source-0.1.2.zip) = 63620 diff --git a/biology/haplohseq/files/patch-makefile b/biology/haplohseq/files/patch-makefile new file mode 100644 index 000000000000..5387716aa503 --- /dev/null +++ b/biology/haplohseq/files/patch-makefile @@ -0,0 +1,105 @@ +--- makefile.orig 2019-08-29 18:03:23 UTC ++++ makefile +@@ -7,23 +7,32 @@ + # + + # Constants +-CXX=g++ ++# Default to g++ if not set by make args or environment ++CXX?=g++ + #-O0 -g will turn on debugging + #The rule of thumb: + #When you need to debug, use -O0 (and -g to generate debugging symbols.) + #When you are preparing to ship it, use -O2. + #When you use gentoo, use -O3...! + #When you need to put it on an embedded system, use -Os (optimize for size, not for efficiency.) +-CXX_FLAGS=-Wall -g -stdlib=libstdc++ ++# Use canonincal compiler variables, which may be provided by build env ++CXXFLAGS?=-Wall -g -stdlib=libstdc++ + SRC=src + CONF=conf + HMM_SRC=$(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 ############################## + + diff --git a/biology/haplohseq/files/patch-src_HaplohSeq.cpp b/biology/haplohseq/files/patch-src_HaplohSeq.cpp new file mode 100644 index 000000000000..a80ce577f747 --- /dev/null +++ b/biology/haplohseq/files/patch-src_HaplohSeq.cpp @@ -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<std::string, boost::shared_ptr<Hmm> > 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<std::string, boost::shared_ptr<Hmm> > chrHmms; diff --git a/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp b/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp new file mode 100644 index 000000000000..21ea56a8f600 --- /dev/null +++ b/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp @@ -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) { diff --git a/biology/haplohseq/files/run-tests b/biology/haplohseq/files/run-tests new file mode 100644 index 000000000000..1ecc6ebc5e35 --- /dev/null +++ b/biology/haplohseq/files/run-tests @@ -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 diff --git a/biology/haplohseq/pkg-descr b/biology/haplohseq/pkg-descr new file mode 100644 index 000000000000..751d6d58268d --- /dev/null +++ b/biology/haplohseq/pkg-descr @@ -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 diff --git a/biology/hhsuite/Makefile b/biology/hhsuite/Makefile index 07f103c78df9..e2893c58d65f 100644 --- a/biology/hhsuite/Makefile +++ b/biology/hhsuite/Makefile @@ -3,7 +3,7 @@ PORTNAME= hhsuite DISTVERSIONPREFIX= v DISTVERSION= 3.2.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology science MAINTAINER= yuri@FreeBSD.org diff --git a/biology/jellyfish/Makefile b/biology/jellyfish/Makefile index 72abb6bfe9aa..0f29e9b7cdf1 100644 --- a/biology/jellyfish/Makefile +++ b/biology/jellyfish/Makefile @@ -3,7 +3,7 @@ PORTNAME= Jellyfish DISTVERSIONPREFIX= v DISTVERSION= 2.2.10 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp b/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp deleted file mode 100644 index 3732945ef013..000000000000 --- a/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp +++ /dev/null @@ -1,35 +0,0 @@ ---- include/jellyfish/file_header.hpp.orig 2018-04-16 12:46:09 UTC -+++ include/jellyfish/file_header.hpp -@@ -21,6 +21,8 @@ - #include <jellyfish/generic_file_header.hpp> - #include <jellyfish/rectangular_binary_matrix.hpp> - -+using std::string; -+ - namespace jellyfish { - /// A header with jellyfish hash specific entries: size, matrix, etc. - class file_header : public generic_file_header { -@@ -42,7 +44,10 @@ class file_header : public generic_file_header { (publ - - RectangularBinaryMatrix matrix(int i = 1) const { - std::string name("matrix"); -- name += std::to_string((long long int)i); // Cast to make gcc4.4 happy! -+ char buff[100]; -+ // name += std::to_string((long long int)i); // Cast to make gcc4.4 happy! -+ snprintf(buff, 99, "%d", i); -+ name += buff; - const unsigned int r = root_[name]["r"].asUInt(); - const unsigned int c = root_[name]["c"].asUInt(); - if(root_[name]["identity"].asBool()) -@@ -56,7 +61,10 @@ class file_header : public generic_file_header { (publ - - void matrix(const RectangularBinaryMatrix& m, int i = 1) { - std::string name("matrix"); -- name += std::to_string((long long int)i); -+ char buff[100]; -+ // name += std::to_string((long long int)i); -+ snprintf(buff, 99, "%d", i); -+ name += buff; - root_[name].clear(); - root_[name]["r"] = m.r(); - root_[name]["c"] = m.c(); diff --git a/biology/linux-foldingathome/Makefile b/biology/linux-foldingathome/Makefile index 5a5a99874960..fc5dbe0e0e7a 100644 --- a/biology/linux-foldingathome/Makefile +++ b/biology/linux-foldingathome/Makefile @@ -13,6 +13,8 @@ MAINTAINER= ports@FreeBSD.org COMMENT= Distributed client for Protein Folding BROKEN= unfetchable +DEPRECATED= Unfetchable, unmaintained +EXPIRATION_DATE= 2019-10-16 USES= linux ONLY_FOR_ARCHS= i386 amd64 diff --git a/biology/p5-TrimGalore/Makefile b/biology/p5-TrimGalore/Makefile index 7b5f2c4ebf3f..1e23f2e2f87b 100644 --- a/biology/p5-TrimGalore/Makefile +++ b/biology/p5-TrimGalore/Makefile @@ -1,7 +1,7 @@ # $FreeBSD$ PORTNAME= TrimGalore -DISTVERSION= 0.6.1 +DISTVERSION= 0.6.4 CATEGORIES= biology perl5 python PKGNAMEPREFIX= p5- @@ -11,7 +11,7 @@ COMMENT= Wrapper around Cutadapt and FastQC for adapter and quality trimming LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cutadapt>0:biology/py-cutadapt@${PY_FLAVOR} \ +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cutadapt>=2.5:biology/py-cutadapt@${PY_FLAVOR} \ fastqc>0:biology/fastqc # Future: Can 3.4+ be determined from cutadapt dep? diff --git a/biology/p5-TrimGalore/distinfo b/biology/p5-TrimGalore/distinfo index da6ec9ed81ef..f3f6ad7e3cf2 100644 --- a/biology/p5-TrimGalore/distinfo +++ b/biology/p5-TrimGalore/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1553345061 -SHA256 (FelixKrueger-TrimGalore-0.6.1_GH0.tar.gz) = 658578c29d007fe66f9ab49608442be703a6fcf535db06eb82659c7edccb62b0 -SIZE (FelixKrueger-TrimGalore-0.6.1_GH0.tar.gz) = 26825390 +TIMESTAMP = 1568381106 +SHA256 (FelixKrueger-TrimGalore-0.6.4_GH0.tar.gz) = eb57e18203d8a1dce1397b930a348a9969eebaa758b8a7304d04c22f216cea2d +SIZE (FelixKrueger-TrimGalore-0.6.4_GH0.tar.gz) = 26827580 diff --git a/biology/py-fastTSNE/Makefile b/biology/py-fastTSNE/Makefile index 0a647f0e023a..8ba0ef155b22 100644 --- a/biology/py-fastTSNE/Makefile +++ b/biology/py-fastTSNE/Makefile @@ -2,7 +2,7 @@ PORTNAME= fastTSNE DISTVERSION= 0.2.13 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-multiqc/Makefile b/biology/py-multiqc/Makefile new file mode 100644 index 000000000000..ff2051382123 --- /dev/null +++ b/biology/py-multiqc/Makefile @@ -0,0 +1,36 @@ +# $FreeBSD$ + +PORTNAME= multiqc +DISTVERSION= 1.7 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Aggregate bioinformatics analysis reports across samples and tools + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}click>0:devel/py-click@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}future>0.14.0:devel/py-future@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.1.1:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}markdown>0:textproc/py-markdown@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}requests>:www/py-requests@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}simplejson>0:devel/py-simplejson@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}Jinja2>=2.9:devel/py-Jinja2@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lzstring>0:archivers/py-lzstring@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}spectra>=0.0.10:graphics/py-spectra@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}colormath>0:math/py-colormath@${PY_FLAVOR} + +USES= python +USE_PYTHON= autoplist concurrent distutils + +NO_ARCH= yes + +post-patch: + @${RM} ${WRKSRC}/multiqc/utils/config.py.orig + +.include <bsd.port.mk> diff --git a/biology/py-multiqc/distinfo b/biology/py-multiqc/distinfo new file mode 100644 index 000000000000..adbaecddc9c9 --- /dev/null +++ b/biology/py-multiqc/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1569116068 +SHA256 (multiqc-1.7.tar.gz) = 02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68 +SIZE (multiqc-1.7.tar.gz) = 1168389 diff --git a/biology/py-multiqc/files/patch-multiqc_utils_config.py b/biology/py-multiqc/files/patch-multiqc_utils_config.py new file mode 100644 index 000000000000..707b510672f0 --- /dev/null +++ b/biology/py-multiqc/files/patch-multiqc_utils_config.py @@ -0,0 +1,41 @@ +--- multiqc/utils/config.py.orig 2019-09-22 13:24:47 UTC ++++ multiqc/utils/config.py +@@ -42,13 +42,13 @@ MULTIQC_DIR = os.path.dirname(os.path.realpath(inspect + # Default MultiQC config + searchp_fn = os.path.join( MULTIQC_DIR, 'utils', 'config_defaults.yaml') + with open(searchp_fn) as f: +- configs = yaml.load(f) ++ configs = yaml.load(f, Loader=yaml.FullLoader) + for c, v in configs.items(): + globals()[c] = v + # Module filename search patterns + searchp_fn = os.path.join( MULTIQC_DIR, 'utils', 'search_patterns.yaml') + with open(searchp_fn) as f: +- sp = yaml.load(f) ++ sp = yaml.load(f, Loader=yaml.FullLoader) + + # Other defaults that can't be set in YAML + data_tmp_dir = '/tmp' # will be overwritten by core script +@@ -118,7 +118,7 @@ def mqc_load_config(yaml_config): + if os.path.isfile(yaml_config): + try: + with open(yaml_config) as f: +- new_config = yaml.load(f) ++ new_config = yaml.load(f, Loader=yaml.FullLoader) + logger.debug("Loading config settings from: {}".format(yaml_config)) + mqc_add_config(new_config, yaml_config) + except (IOError, AttributeError) as e: +@@ -132,11 +132,11 @@ def mqc_load_config(yaml_config): + def mqc_cl_config(cl_config): + for clc_str in cl_config: + try: +- parsed_clc = yaml.load(clc_str) ++ parsed_clc = yaml.load(clc_str, Loader=yaml.FullLoader) + # something:var fails as it needs a space. Fix this (a common mistake) + if isinstance(parsed_clc, str) and ':' in clc_str: + clc_str = ': '.join(clc_str.split(':')) +- parsed_clc = yaml.load(clc_str) ++ parsed_clc = yaml.load(clc_str, Loader=yaml.FullLoader) + assert(isinstance(parsed_clc, dict)) + except yaml.scanner.ScannerError as e: + logger.error("Could not parse command line config: {}\n{}".format(clc_str, e)) diff --git a/biology/py-multiqc/files/patch-scripts_multiqc b/biology/py-multiqc/files/patch-scripts_multiqc new file mode 100644 index 000000000000..34eef2e89279 --- /dev/null +++ b/biology/py-multiqc/files/patch-scripts_multiqc @@ -0,0 +1,32 @@ +--- scripts/multiqc.orig 2018-12-21 17:29:54 UTC ++++ scripts/multiqc +@@ -6,18 +6,26 @@ + from __future__ import print_function + + import base64 +-import click ++import os ++import sys ++ ++if 'LC_ALL' in os.environ and 'LANG' in os.environ: ++ import click ++else: ++ print('multiqc: LC_ALL and LANG must be set to a UTF-8 character set') ++ print('in your environment in order for the click module to function.') ++ print('E.g. export LC_ALL=en_US.UTF-8 or setenv LC_ALL en_US.UTF-8') ++ sys.exit() ++ + from distutils import version + from distutils.dir_util import copy_tree + import errno + import io + import jinja2 +-import os + import pkg_resources + import re + import shutil + import subprocess +-import sys + import tempfile + import traceback + diff --git a/biology/py-multiqc/pkg-descr b/biology/py-multiqc/pkg-descr new file mode 100644 index 000000000000..399f8a41c313 --- /dev/null +++ b/biology/py-multiqc/pkg-descr @@ -0,0 +1,5 @@ +MultiQC searches a given directory for analysis logs and compiles an HTML +report. It's a general use tool, perfect for summarising the output from +numerous bioinformatics tools. + +WWW: https://pypi.python.org/pypi/multiqc diff --git a/biology/seqan1/Makefile b/biology/seqan1/Makefile index a256864ec0d9..df8fb2117675 100644 --- a/biology/seqan1/Makefile +++ b/biology/seqan1/Makefile @@ -12,7 +12,7 @@ MAINTAINER= h2+fbsdports@fsfe.org COMMENT= C++ Sequence Analysis Library LICENSE= BSD3CLAUSE -LICENSE_FILE_BSD=${WRKSRC}/seqan/LICENSE +LICENSE_FILE_BSD3CLAUSE= ${WRKSRC}/seqan/LICENSE USES= zip NO_BUILD= yes diff --git a/biology/trimmomatic/Makefile b/biology/trimmomatic/Makefile index d567d2499074..b180fe8b3e96 100644 --- a/biology/trimmomatic/Makefile +++ b/biology/trimmomatic/Makefile @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= trimmomatic -PORTVERSION= 0.35 +DISTVERSION= 0.39 CATEGORIES= biology java MASTER_SITES= http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/ DISTNAME= Trimmomatic-${PORTVERSION} @@ -11,17 +11,22 @@ MAINTAINER= jwb@FreeBSD.org COMMENT= Flexible read trimming tool for Illumina NGS data LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE USES= zip USE_JAVA= yes + JAVA_VERSION= 1.6+ JAVA_RUN= yes NO_BUILD= yes NO_ARCH= yes +SUB_FILES= trimmomatic + do-install: ${INSTALL_DATA} ${WRKSRC}/trimmomatic-${PORTVERSION}.jar \ ${STAGEDIR}${JAVAJARDIR}/trimmomatic.jar cd ${WRKSRC} && ${COPYTREE_SHARE} adapters ${STAGEDIR}${DATADIR} + ${INSTALL_SCRIPT} ${WRKDIR}/trimmomatic ${STAGEDIR}${PREFIX}/bin .include <bsd.port.mk> diff --git a/biology/trimmomatic/distinfo b/biology/trimmomatic/distinfo index fc50ab760f76..5eb8a5dd06f1 100644 --- a/biology/trimmomatic/distinfo +++ b/biology/trimmomatic/distinfo @@ -1,2 +1,3 @@ -SHA256 (Trimmomatic-0.35.zip) = 43b993ffa91c039b529db8334bc6aa4b0d601e69c79aaa9a1457ecd1c2c3cc69 -SIZE (Trimmomatic-0.35.zip) = 129810 +TIMESTAMP = 1568469691 +SHA256 (Trimmomatic-0.39.zip) = 2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca +SIZE (Trimmomatic-0.39.zip) = 133596 diff --git a/biology/trimmomatic/files/trimmomatic.in b/biology/trimmomatic/files/trimmomatic.in new file mode 100644 index 000000000000..24a6e7c7ff5c --- /dev/null +++ b/biology/trimmomatic/files/trimmomatic.in @@ -0,0 +1,3 @@ +#!/bin/sh -e + +java -jar %%PREFIX%%/share/java/classes/trimmomatic.jar "$@" diff --git a/biology/trimmomatic/pkg-plist b/biology/trimmomatic/pkg-plist index be4315845557..715fe3513733 100644 --- a/biology/trimmomatic/pkg-plist +++ b/biology/trimmomatic/pkg-plist @@ -1,7 +1,8 @@ +bin/trimmomatic +%%JAVAJARDIR%%/trimmomatic.jar %%DATADIR%%/adapters/NexteraPE-PE.fa %%DATADIR%%/adapters/TruSeq2-PE.fa %%DATADIR%%/adapters/TruSeq2-SE.fa %%DATADIR%%/adapters/TruSeq3-PE-2.fa %%DATADIR%%/adapters/TruSeq3-PE.fa %%DATADIR%%/adapters/TruSeq3-SE.fa -%%JAVAJARDIR%%/trimmomatic.jar |