Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 468100) +++ head/biology/Makefile (revision 468101) @@ -1,136 +1,137 @@ # $FreeBSD$ # 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 += vcftools SUBDIR += vcflib SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/pbcopper/Makefile =================================================================== --- head/biology/pbcopper/Makefile (nonexistent) +++ head/biology/pbcopper/Makefile (revision 468101) @@ -0,0 +1,28 @@ +# $FreeBSD$ + +PORTNAME= pbcopper +DISTVERSION= g20180413 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Core C++ library for Pacific Biosciences tools + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +LIB_DEPENDS= libboost_regex.so:devel/boost-libs + +USES= cmake +# Although there are a couple releases, git describe --tags does not work +# so we cannot use the usual USE_GITHUB tools here. +USE_GITHUB= yes +GH_ACCOUNT= PacificBiosciences +GH_TAGNAME= 17ef457a0dbe1894a8d17af7ddba01a6261bf117 + +do-install: + ${INSTALL_DATA} ${BUILD_WRKSRC}/lib/*.a ${STAGEDIR}${PREFIX}/lib + cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include + ${MV} ${STAGEDIR}${PREFIX}/include/meson.build \ + ${STAGEDIR}${PREFIX}/include/pbcopper + +.include Property changes on: head/biology/pbcopper/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/pbcopper/distinfo =================================================================== --- head/biology/pbcopper/distinfo (nonexistent) +++ head/biology/pbcopper/distinfo (revision 468101) @@ -0,0 +1,3 @@ +TIMESTAMP = 1524500014 +SHA256 (PacificBiosciences-pbcopper-g20180413-17ef457a0dbe1894a8d17af7ddba01a6261bf117_GH0.tar.gz) = 13f006d53334a0538657e0ba5c6e02f811f1901cd25fce220fc9011726ffe23f +SIZE (PacificBiosciences-pbcopper-g20180413-17ef457a0dbe1894a8d17af7ddba01a6261bf117_GH0.tar.gz) = 3033636 Property changes on: head/biology/pbcopper/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/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake =================================================================== --- head/biology/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake (nonexistent) +++ head/biology/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake (revision 468101) @@ -0,0 +1,21 @@ +--- cmake/pbcopper-gitsha1.cmake.orig 2018-03-16 16:16:38 UTC ++++ cmake/pbcopper-gitsha1.cmake +@@ -5,16 +5,15 @@ endif() + set(__find_git_sha1 YES) + + function(find_git_sha1 _GIT_SHA1) +- find_package(Git QUIET REQUIRED) + execute_process(COMMAND +- "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=*" ++ echo ce9a4b6 + WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" + RESULT_VARIABLE res + OUTPUT_VARIABLE out + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + if (NOT res EQUAL 0) +- message(FATAL_ERROR "Could not determine git sha1 via `git describe --always --dirty=*`") ++ message(FATAL_ERROR "Could not determine git sha1") + endif() + set(${_GIT_SHA1} "${out}" PARENT_SCOPE) + endfunction() Property changes on: head/biology/pbcopper/files/patch-cmake_pbcopper-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/pbcopper/pkg-descr =================================================================== --- head/biology/pbcopper/pkg-descr (nonexistent) +++ head/biology/pbcopper/pkg-descr (revision 468101) @@ -0,0 +1,5 @@ +The pbcopper library provides a suite of data structures, algorithms, and +utilities for C++ applications. It is a core component of Pacific Biosciences +genomics analysis tools. + +WWW: https://github.com/PacificBiosciences/pbcopper Property changes on: head/biology/pbcopper/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/pbcopper/pkg-plist =================================================================== --- head/biology/pbcopper/pkg-plist (nonexistent) +++ head/biology/pbcopper/pkg-plist (revision 468101) @@ -0,0 +1,75 @@ +include/pbcopper/PbcopperConfig.h +include/pbcopper/align/Seed.h +include/pbcopper/align/Seeds.h +include/pbcopper/align/internal/Seed-inl.h +include/pbcopper/align/internal/Seeds-inl.h +include/pbcopper/cli/CLI.h +include/pbcopper/cli/HelpPrinter.h +include/pbcopper/cli/Interface.h +include/pbcopper/cli/Option.h +include/pbcopper/cli/OptionFlags.h +include/pbcopper/cli/Parser.h +include/pbcopper/cli/PositionalArg.h +include/pbcopper/cli/Results.h +include/pbcopper/cli/SingleDashMode.h +include/pbcopper/cli/VersionPrinter.h +include/pbcopper/cli/internal/Option-inl.h +include/pbcopper/cli/toolcontract/Config.h +include/pbcopper/cli/toolcontract/Driver.h +include/pbcopper/cli/toolcontract/InputFileType.h +include/pbcopper/cli/toolcontract/JsonPrinter.h +include/pbcopper/cli/toolcontract/OutputFileType.h +include/pbcopper/cli/toolcontract/ResolvedToolContract.h +include/pbcopper/cli/toolcontract/ResourceType.h +include/pbcopper/cli/toolcontract/Task.h +include/pbcopper/cli/toolcontract/TaskType.h +include/pbcopper/cli/toolcontract/internal/Config-inl.h +include/pbcopper/cli/toolcontract/internal/Driver-inl.h +include/pbcopper/cli/toolcontract/internal/InputFileType-inl.h +include/pbcopper/cli/toolcontract/internal/OutputFileType-inl.h +include/pbcopper/cli/toolcontract/internal/Task-inl.h +include/pbcopper/data/CCSTag.h +include/pbcopper/data/Cigar.h +include/pbcopper/data/CigarOperation.h +include/pbcopper/data/Interval.h +include/pbcopper/data/MovieName.h +include/pbcopper/data/Position.h +include/pbcopper/data/RSMovieName.h +include/pbcopper/data/RSReadName.h +include/pbcopper/data/ReadName.h +include/pbcopper/data/Zmw.h +include/pbcopper/data/internal/CigarOperation-inl.h +include/pbcopper/data/internal/Interval-inl.h +include/pbcopper/data/internal/MovieName-inl.h +include/pbcopper/data/internal/RSMovieName-inl.h +include/pbcopper/data/internal/ReadNameBase-inl.h +include/pbcopper/data/internal/ReadNameBase.h +include/pbcopper/json/JSON.h +include/pbcopper/json/internal/json.hpp +include/pbcopper/logging/Logging.h +include/pbcopper/logging/internal/Logging-inl.h +include/pbcopper/meson.build +include/pbcopper/parallel/FireAndForget.h +include/pbcopper/parallel/WorkQueue.h +include/pbcopper/qgram/Index.h +include/pbcopper/qgram/IndexHit.h +include/pbcopper/qgram/IndexHits.h +include/pbcopper/qgram/internal/Hashing-inl.h +include/pbcopper/qgram/internal/Index-inl.h +include/pbcopper/stream/Stream.h +include/pbcopper/utility/CallbackTimer.h +include/pbcopper/utility/EnumClassHash.h +include/pbcopper/utility/FileUtils.h +include/pbcopper/utility/MoveAppend.h +include/pbcopper/utility/PbcopperVersion.h +include/pbcopper/utility/SafeSubtract.h +include/pbcopper/utility/Stopwatch.h +include/pbcopper/utility/StringUtils.h +include/pbcopper/utility/SystemInfo.h +include/pbcopper/utility/Unused.h +include/pbcopper/utility/internal/CallbackTimer-inl.h +include/pbcopper/utility/internal/FileUtils-inl.h +include/pbcopper/utility/internal/Stopwatch-inl.h +include/pbcopper/utility/internal/StringUtils-inl.h +include/pbcopper/utility/internal/SystemInfo-inl.h +lib/libpbcopper.a Property changes on: head/biology/pbcopper/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