Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 468099) +++ head/biology/Makefile (revision 468100) @@ -1,135 +1,136 @@ # $FreeBSD$ # 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 += 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/pbbam/Makefile =================================================================== --- head/biology/pbbam/Makefile (nonexistent) +++ head/biology/pbbam/Makefile (revision 468100) @@ -0,0 +1,35 @@ +# $FreeBSD$ + +PORTNAME= pbbam +DISTVERSION= g20180416 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= PacBio BAM C++ library, with SWIG bindings + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +BUILD_DEPENDS= boost-libs>=1.60.0:devel/boost-libs +LIB_DEPENDS= libhts.so:biology/htslib \ + libboost_regex.so:devel/boost-libs + +USES= cmake pkgconfig +USE_GITHUB= yes +GH_ACCOUNT= PacificBiosciences +GH_TAGNAME= c6b8113adb5104948879e9ff69f739121f12a09f + +# Disable tests for now. Bound to bundled googletest. +CMAKE_ARGS+= -DHTSLIB_INCLUDE_DIRS:STRING=${LOCALBASE}/include/htslib \ + -DHTSLIB_LIBRARIES:STRING="-L${LOCALBASE}/lib -lhts" \ + -DPacBioBAM_build_tests:BOOL=OFF \ + -DPacBioBAM_build_docs:BOOL=OFF + +do-install: + ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin + ${INSTALL_DATA} ${BUILD_WRKSRC}/lib/* ${STAGEDIR}${PREFIX}/lib + cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include + ${MV} ${STAGEDIR}${PREFIX}/include/meson.build \ + ${STAGEDIR}${PREFIX}/include/pbbam + +.include Property changes on: head/biology/pbbam/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/pbbam/distinfo =================================================================== --- head/biology/pbbam/distinfo (nonexistent) +++ head/biology/pbbam/distinfo (revision 468100) @@ -0,0 +1,3 @@ +TIMESTAMP = 1524331626 +SHA256 (PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz) = f7ede42417110db4fcc3fbc4b837911a0e2242e541a88c8ac34b4c26b4e5aad4 +SIZE (PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz) = 8105156 Property changes on: head/biology/pbbam/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/pbbam/pkg-descr =================================================================== --- head/biology/pbbam/pkg-descr (nonexistent) +++ head/biology/pbbam/pkg-descr (revision 468100) @@ -0,0 +1,11 @@ +As of the 3.0 release of SMRTanalysis, PacBio is embracing the industry +standard BAM format for (both aligned and unaligned) basecall data files. We +have also formulated a BAM companion file format (bam.pbi) enabling fast access +to a richer set of per-read information as well as compatibility for software +built around the legacy cmp.h5 format. + +The pbbam software package provides components to create, query, & edit PacBio +BAM files and associated indices. These components include a core C++ library, +bindings for additional languages, and command-line utilities. + +WWW: https://github.com/PacificBiosciences/pbbam Property changes on: head/biology/pbbam/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/pbbam/pkg-plist =================================================================== --- head/biology/pbbam/pkg-plist (nonexistent) +++ head/biology/pbbam/pkg-plist (revision 468100) @@ -0,0 +1,132 @@ +bin/bam2sam +bin/pbbamify +bin/pbindex +bin/pbindexdump +bin/pbmerge +include/pbbam/Accuracy.h +include/pbbam/AlignmentPrinter.h +include/pbbam/BaiIndexedBamReader.h +include/pbbam/BamFile.h +include/pbbam/BamHeader.h +include/pbbam/BamReader.h +include/pbbam/BamRecord.h +include/pbbam/BamRecordBuilder.h +include/pbbam/BamRecordImpl.h +include/pbbam/BamRecordTag.h +include/pbbam/BamRecordView.h +include/pbbam/BamTagCodec.h +include/pbbam/BamWriter.h +include/pbbam/BarcodeQuery.h +include/pbbam/Cigar.h +include/pbbam/CigarOperation.h +include/pbbam/ClipType.h +include/pbbam/Compare.h +include/pbbam/CompositeBamReader.h +include/pbbam/CompositeFastaReader.h +include/pbbam/Config.h +include/pbbam/DataSet.h +include/pbbam/DataSetTypes.h +include/pbbam/DataSetXsd.h +include/pbbam/EntireFileQuery.h +include/pbbam/FastaReader.h +include/pbbam/FastaSequence.h +include/pbbam/FastaSequenceQuery.h +include/pbbam/FastqReader.h +include/pbbam/FastqSequence.h +include/pbbam/FrameEncodingType.h +include/pbbam/Frames.h +include/pbbam/GenomicInterval.h +include/pbbam/GenomicIntervalQuery.h +include/pbbam/IRecordWriter.h +include/pbbam/IndexedBamWriter.h +include/pbbam/IndexedFastaReader.h +include/pbbam/Interval.h +include/pbbam/LocalContextFlags.h +include/pbbam/MD5.h +include/pbbam/MakeUnique.h +include/pbbam/MoveAppend.h +include/pbbam/Orientation.h +include/pbbam/PbiBasicTypes.h +include/pbbam/PbiBuilder.h +include/pbbam/PbiFile.h +include/pbbam/PbiFilter.h +include/pbbam/PbiFilterQuery.h +include/pbbam/PbiFilterTypes.h +include/pbbam/PbiIndexedBamReader.h +include/pbbam/PbiRawData.h +include/pbbam/Position.h +include/pbbam/ProgramInfo.h +include/pbbam/PulseBehavior.h +include/pbbam/PulseExclusionReason.h +include/pbbam/QNameQuery.h +include/pbbam/QualityValue.h +include/pbbam/QualityValues.h +include/pbbam/ReadAccuracyQuery.h +include/pbbam/ReadGroupInfo.h +include/pbbam/RecordType.h +include/pbbam/SamTagCodec.h +include/pbbam/SamWriter.h +include/pbbam/SequenceInfo.h +include/pbbam/Strand.h +include/pbbam/StringUtilities.h +include/pbbam/SubreadLengthQuery.h +include/pbbam/Tag.h +include/pbbam/TagCollection.h +include/pbbam/Unused.h +include/pbbam/Validator.h +include/pbbam/ZmwGroupQuery.h +include/pbbam/ZmwQuery.h +include/pbbam/ZmwType.h +include/pbbam/ZmwTypeMap.h +include/pbbam/exception/BundleChemistryMappingException.h +include/pbbam/exception/InvalidSequencingChemistryException.h +include/pbbam/exception/ValidationException.h +include/pbbam/internal/Accuracy.inl +include/pbbam/internal/BamHeader.inl +include/pbbam/internal/BamRecord.inl +include/pbbam/internal/BamRecordBuilder.inl +include/pbbam/internal/BamRecordImpl.inl +include/pbbam/internal/BamRecordView.inl +include/pbbam/internal/Cigar.inl +include/pbbam/internal/CigarOperation.inl +include/pbbam/internal/Compare.inl +include/pbbam/internal/CompositeBamReader.inl +include/pbbam/internal/CompositeFastaReader.inl +include/pbbam/internal/DataSet.inl +include/pbbam/internal/DataSetBaseTypes.h +include/pbbam/internal/DataSetBaseTypes.inl +include/pbbam/internal/DataSetElement.h +include/pbbam/internal/DataSetElement.inl +include/pbbam/internal/DataSetListElement.h +include/pbbam/internal/DataSetListElement.inl +include/pbbam/internal/DataSetTypes.inl +include/pbbam/internal/FastaSequence.inl +include/pbbam/internal/FastqSequence.inl +include/pbbam/internal/Frames.inl +include/pbbam/internal/GenomicInterval.inl +include/pbbam/internal/Interval.inl +include/pbbam/internal/PbiBasicTypes.inl +include/pbbam/internal/PbiFilter.inl +include/pbbam/internal/PbiFilterTypes.inl +include/pbbam/internal/PbiRawData.inl +include/pbbam/internal/ProgramInfo.inl +include/pbbam/internal/QualityValue.inl +include/pbbam/internal/QualityValues.inl +include/pbbam/internal/QueryBase.h +include/pbbam/internal/QueryBase.inl +include/pbbam/internal/ReadGroupInfo.inl +include/pbbam/internal/SequenceInfo.inl +include/pbbam/internal/Tag.inl +include/pbbam/internal/Validator.inl +include/pbbam/meson.build +include/pbbam/virtual/VirtualPolymeraseBamRecord.h +include/pbbam/virtual/VirtualPolymeraseCompositeReader.h +include/pbbam/virtual/VirtualPolymeraseReader.h +include/pbbam/virtual/VirtualRegion.h +include/pbbam/virtual/VirtualRegionType.h +include/pbbam/virtual/VirtualRegionTypeMap.h +include/pbbam/virtual/VirtualZmwBamRecord.h +include/pbbam/virtual/WhitelistedZmwReadStitcher.h +include/pbbam/virtual/ZmwReadStitcher.h +include/pbbam/virtual/ZmwWhitelistVirtualReader.h +lib/libpbbam.a Property changes on: head/biology/pbbam/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