Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 562035) +++ head/biology/Makefile (revision 562036) @@ -1,186 +1,187 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bioawk SUBDIR += biococoa SUBDIR += bioparser SUBDIR += biosoup SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += clustal-omega SUBDIR += clustalw 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 += gcta 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-DB-EMBL SUBDIR += p5-Bio-DB-NCBIHelper 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-Bio-Variation SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += picard-tools SUBDIR += plink SUBDIR += pooler 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-ete3 SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman + SUBDIR += spoa SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include Index: head/biology/spoa/Makefile =================================================================== --- head/biology/spoa/Makefile (nonexistent) +++ head/biology/spoa/Makefile (revision 562036) @@ -0,0 +1,38 @@ +# $FreeBSD$ + +PORTNAME= spoa +DISTVERSION= 4.0.7 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= C++ implementation of the partial order alignment (POA) algorithm + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= bioparser>0:biology/bioparser \ + ${LOCALBASE}/include/biosoup/nucleic_acid.hpp:biology/biosoup \ + cereal>0:devel/cereal \ + cpu_features>0:devel/cpu_features \ + simde>0:devel/simde +RUN_DEPENDS= cereal>0:devel/cereal +TEST_DEPENDS= googletest>0:devel/googletest + +USES= cmake compiler:c++11-lang localbase:ldflags +USE_LDCONFIG= yes + +USE_GITHUB= yes +GH_ACCOUNT= rvaser + +CMAKE_ON= BUILD_SHARED_LIBS spoa_optimize_for_portability spoa_build_executable spoa_use_simde spoa_use_simde_nonvec spoa_use_simde_openmp spoa_generate_dispatch +CMAKE_OFF= spoa_optimize_for_native + +LDFLAGS+= -lz -lcpu_features + +do-test: + @cd ${BUILD_WRKSRC} && \ + ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -D${PORTNAME}_build_tests:BOOL=ON ${CMAKE_SOURCE_PATH} && \ + ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ + ${BUILD_WRKSRC}/bin/${PORTNAME}_test + +.include Property changes on: head/biology/spoa/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/spoa/distinfo =================================================================== --- head/biology/spoa/distinfo (nonexistent) +++ head/biology/spoa/distinfo (revision 562036) @@ -0,0 +1,3 @@ +TIMESTAMP = 1611045674 +SHA256 (rvaser-spoa-4.0.7_GH0.tar.gz) = f8cb409adcca20ca6cc0025371743b915790879957cf001ca5e155ed16fd14e0 +SIZE (rvaser-spoa-4.0.7_GH0.tar.gz) = 43574 Property changes on: head/biology/spoa/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/spoa/files/patch-CMakeLists.txt =================================================================== --- head/biology/spoa/files/patch-CMakeLists.txt (nonexistent) +++ head/biology/spoa/files/patch-CMakeLists.txt (revision 562036) @@ -0,0 +1,107 @@ +--- CMakeLists.txt.orig 2021-01-15 03:44:02 UTC ++++ CMakeLists.txt +@@ -44,9 +44,10 @@ if (spoa_use_simde OR + endif () + endif () + +-if (NOT TARGET cereal) +- add_subdirectory(vendor/cereal EXCLUDE_FROM_ALL) +-endif () ++#if (NOT TARGET cereal) ++# add_subdirectory(vendor/cereal EXCLUDE_FROM_ALL) ++#endif () ++find_package(cereal REQUIRED) + + add_library(${PROJECT_NAME} + src/alignment_engine.cpp +@@ -55,8 +56,8 @@ add_library(${PROJECT_NAME} + src/dispatcher.cpp) + target_include_directories(${PROJECT_NAME} PUBLIC + $ +- $ +- $ ++ #$ ++ #$ + $) + target_link_libraries(${PROJECT_NAME} + cereal) +@@ -65,9 +66,9 @@ if (BUILD_SHARED_LIBS) + endif () + + if (spoa_generate_dispatch) +- if (NOT TARGET cpu_features) +- add_subdirectory(vendor/cpu_features EXCLUDE_FROM_ALL) +- endif () ++ #if (NOT TARGET cpu_features) ++ # add_subdirectory(vendor/cpu_features EXCLUDE_FROM_ALL) ++ #endif () + + list(APPEND ARCHITECTURES avx2 sse4.1 sse2) + foreach(arch IN LISTS ARCHITECTURES) +@@ -92,8 +93,8 @@ if (spoa_generate_dispatch) + ${PROJECT_NAME}_sse4.1 + ${PROJECT_NAME}_sse2) + +- target_link_libraries(${PROJECT_NAME} +- cpu_features) ++ #target_link_libraries(${PROJECT_NAME} ++ # cpu_features) + endif () + + include(GNUInstallDirs) +@@ -110,18 +111,19 @@ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/spoa-1.pc + + option(spoa_build_executable "Build spoa standalone tool" OFF) + if (spoa_build_executable) +- if (NOT TARGET biosoup) +- add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL) +- endif () +- if (NOT TARGET bioparser) +- add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL) +- endif () ++ #if (NOT TARGET biosoup) ++ # add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL) ++ #endif () ++ #if (NOT TARGET bioparser) ++ # add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL) ++ #endif () + add_executable(${PROJECT_NAME}_exe + src/main.cpp) + target_link_libraries(${PROJECT_NAME}_exe + ${PROJECT_NAME} +- bioparser +- biosoup) ++ #bioparser ++ #biosoup ++ ) + target_compile_definitions(${PROJECT_NAME}_exe PRIVATE + SPOA_VERSION="v${PROJECT_VERSION}") + set_property(TARGET ${PROJECT_NAME}_exe PROPERTY +@@ -134,19 +136,19 @@ endif () + option(spoa_build_tests "Build spoa unit tests" OFF) + if (spoa_build_tests) + find_package(GTest REQUIRED) +- if (NOT TARGET biosoup) +- add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL) +- endif () +- if (NOT TARGET bioparser) +- add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL) +- endif () ++ #if (NOT TARGET biosoup) ++ # add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL) ++ #endif () ++ #if (NOT TARGET bioparser) ++ # add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL) ++ #endif () + include_directories(${PROJECT_SOURCE_DIR}/src) + add_executable(${PROJECT_NAME}_test + test/spoa_test.cpp) + target_link_libraries(${PROJECT_NAME}_test + ${PROJECT_NAME} +- bioparser +- biosoup ++ #bioparser ++ #biosoup + GTest::Main) + target_compile_definitions(${PROJECT_NAME}_test PRIVATE + SPOA_DATA_PATH="${PROJECT_SOURCE_DIR}/test/data/sample.fastq.gz") Property changes on: head/biology/spoa/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/spoa/pkg-descr =================================================================== --- head/biology/spoa/pkg-descr (nonexistent) +++ head/biology/spoa/pkg-descr (revision 562036) @@ -0,0 +1,9 @@ +Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) +algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to +generate consensus sequences. It supports three alignment modes: local +(Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap), +and three gap modes: linear, affine and convex (piecewise affine). It also +supports Intel SSE4.1+ and AVX2 vectorization (marginally faster due to high +latency shifts), SIMDe and dispatching. + +WWW: https://github.com/rvaser/spoa Property changes on: head/biology/spoa/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 Index: head/biology/spoa/pkg-plist =================================================================== --- head/biology/spoa/pkg-plist (nonexistent) +++ head/biology/spoa/pkg-plist (revision 562036) @@ -0,0 +1,8 @@ +bin/spoa +include/spoa/alignment_engine.hpp +include/spoa/architectures.hpp +include/spoa/graph.hpp +include/spoa/spoa.hpp +lib/libspoa.so +lib/libspoa.so.7.0.0 +libdata/pkgconfig/spoa-1.pc Property changes on: head/biology/spoa/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