Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 562032) +++ head/biology/Makefile (revision 562033) @@ -1,184 +1,185 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bioawk SUBDIR += biococoa + SUBDIR += bioparser 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 += 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/bioparser/Makefile =================================================================== --- head/biology/bioparser/Makefile (nonexistent) +++ head/biology/bioparser/Makefile (revision 562033) @@ -0,0 +1,39 @@ +# $FreeBSD$ + +PORTNAME= bioparser +DISTVERSION= 3.0.12 +CATEGORIES= biology devel + +MAINTAINER= yuri@FreeBSD.org +COMMENT= C++ header only parsing library for several formats in bioinformatics + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +TEST_DEPENDS= googletest>0:devel/googletest + +USES= cmake + +USE_GITHUB= yes +GH_ACCOUNT= rvaser +GH_TUPLE= rvaser:biosoup:e2b39f1:biosoup/vendor/biosoup + +NO_ARCH= yes + +PLIST_FILES= include/bioparser/fasta_parser.hpp \ + include/bioparser/fastq_parser.hpp \ + include/bioparser/mhap_parser.hpp \ + include/bioparser/paf_parser.hpp \ + include/bioparser/parser.hpp \ + include/bioparser/sam_parser.hpp + +do-install: + cd ${WRKSRC}/include && ${COPYTREE_SHARE} ${PORTNAME} ${STAGEDIR}${PREFIX}/include + +do-test: + @cd ${BUILD_WRKSRC} && \ + ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -Dbioparser_build_tests:BOOL=ON ${CMAKE_SOURCE_PATH} && \ + ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ + ${BUILD_WRKSRC}/bin/bioparser_test + +.include Property changes on: head/biology/bioparser/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/bioparser/distinfo =================================================================== --- head/biology/bioparser/distinfo (nonexistent) +++ head/biology/bioparser/distinfo (revision 562033) @@ -0,0 +1,5 @@ +TIMESTAMP = 1611042654 +SHA256 (rvaser-bioparser-3.0.12_GH0.tar.gz) = 00672e3dfa4946c37df8818d283742b51f21c8a0c70ddac543b241d6ba54dbcb +SIZE (rvaser-bioparser-3.0.12_GH0.tar.gz) = 1013329 +SHA256 (rvaser-biosoup-e2b39f1_GH0.tar.gz) = fe122e65d1691ca781584d8bb42538c5904852ccbb1ec48bc13aa2652b0f9ddc +SIZE (rvaser-biosoup-e2b39f1_GH0.tar.gz) = 6979 Property changes on: head/biology/bioparser/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/bioparser/pkg-descr =================================================================== --- head/biology/bioparser/pkg-descr (nonexistent) +++ head/biology/bioparser/pkg-descr (revision 562033) @@ -0,0 +1,4 @@ +Bioparser is a C++ header only parsing library for several formats in +bioinformatics (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files. + +WWW: https://github.com/rvaser/bioparser Property changes on: head/biology/bioparser/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