diff --git a/biology/Makefile b/biology/Makefile index 294a87ca4e78..e24861f2a317 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,216 +1,217 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bfc SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += biolibc-tools SUBDIR += bioparser SUBDIR += biosig SUBDIR += biosoup SUBDIR += biostar-tools 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 += edlib SUBDIR += emboss SUBDIR += erminej SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += flash SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan 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 += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils + SUBDIR += libnuml SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += mmseqs2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-entrez-direct SUBDIR += ncbi-toolkit SUBDIR += ncbi-vdb 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 += peak-classifier SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred 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-PySCeS SUBDIR += py-bigwig SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-goatools SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-ont-fast5-api SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-python-libsbml SUBDIR += py-pywgsim SUBDIR += py-resdk SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler SUBDIR += readseq SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += sam2pairwise SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqan3 SUBDIR += seqio SUBDIR += seqkit SUBDIR += seqtk SUBDIR += sigviewer SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += snpeff SUBDIR += spoa SUBDIR += sra-tools SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += taxonkit SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ucsc-userapps SUBDIR += ugene SUBDIR += unikmer SUBDIR += vcf-split SUBDIR += vcf2hap SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include diff --git a/biology/libnuml/Makefile b/biology/libnuml/Makefile new file mode 100644 index 000000000000..890a2e919ee8 --- /dev/null +++ b/biology/libnuml/Makefile @@ -0,0 +1,26 @@ +PORTNAME= libnuml +DISTVERSIONPREFIX= v +DISTVERSION= 1.1.4 +CATEGORIES= biology devel + +MAINTAINER= yuri@FreeBSD.org +COMMENT= C++ library for Numerical Markup Language + +LICENSE= LGPL21 + +LIB_DEPENDS= libsbml.so:biology/libsbml + +USES= cmake gnome +USE_GNOME= libxml2 +USE_LDCONFIG= yes + +USE_GITHUB= yes +GH_ACCOUNT= NuML +GH_PROJECT= NuML + +WRKSRC_SUBDIR= ${PORTNAME} + +post-install: + @${RM} -r ${STAGEDIR}${DATADIR} + +.include diff --git a/biology/libnuml/distinfo b/biology/libnuml/distinfo new file mode 100644 index 000000000000..6d10a1bca0ea --- /dev/null +++ b/biology/libnuml/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1632027367 +SHA256 (NuML-NuML-v1.1.4_GH0.tar.gz) = 18e8f6d9b0c261f34123bc2e1bd601730993d63fb53f7434b5901b1059aa9109 +SIZE (NuML-NuML-v1.1.4_GH0.tar.gz) = 3419841 diff --git a/biology/libnuml/pkg-descr b/biology/libnuml/pkg-descr new file mode 100644 index 000000000000..011a4793507b --- /dev/null +++ b/biology/libnuml/pkg-descr @@ -0,0 +1,6 @@ +The Numerical Markup Language (NuML) aims to standardize the exchange and +archiving of numerical results. NuML originates from the numerical aspects of +the Systems Biology Results Markup Language (SBRML) with the aim of re-using it +in multiple other standardization efforts. + +WWW: https://github.com/NuML/NuML diff --git a/biology/libnuml/pkg-plist b/biology/libnuml/pkg-plist new file mode 100644 index 000000000000..44b188050119 --- /dev/null +++ b/biology/libnuml/pkg-plist @@ -0,0 +1,44 @@ +include/numl/AtomicDescription.h +include/numl/AtomicValue.h +include/numl/CompositeDescription.h +include/numl/CompositeValue.h +include/numl/Dimension.h +include/numl/DimensionDescription.h +include/numl/NMBase.h +include/numl/NUMLDocument.h +include/numl/NUMLError.h +include/numl/NUMLErrorLog.h +include/numl/NUMLErrorTable.h +include/numl/NUMLList.h +include/numl/NUMLNamespaces.h +include/numl/NUMLReader.h +include/numl/NUMLSimpleTester.h +include/numl/NUMLTypeCodes.h +include/numl/NUMLTypes.h +include/numl/NUMLVisitor.h +include/numl/NUMLWriter.h +include/numl/OntologyTerm.h +include/numl/ResultComponent.h +include/numl/Tuple.h +include/numl/TupleDescription.h +include/numl/common/common.h +include/numl/common/extern.h +include/numl/common/libnuml-config-common.h +include/numl/common/libnuml-config-unix.h +include/numl/common/libnuml-config-win.h +include/numl/common/libnuml-config.h +include/numl/common/libnuml-namespace.h +include/numl/common/libnuml-package.h +include/numl/common/libnuml-version.h +include/numl/common/numlfwd.h +include/numl/common/operationReturnValues.h +lib/cmake/numl-config-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/numl-config-version.cmake +lib/cmake/numl-config.cmake +lib/cmake/numl-static-config-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/numl-static-config-version.cmake +lib/cmake/numl-static-config.cmake +lib/libnuml-static.a +lib/libnuml.so +lib/libnuml.so.1 +lib/libnuml.so.1.1.4