diff --git a/biology/Makefile b/biology/Makefile index ec370d664a52..f57fe3e300fd 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,218 +1,219 @@ 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 += libsedml 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-libnuml 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/libsedml/Makefile b/biology/libsedml/Makefile new file mode 100644 index 000000000000..6f13d1379a99 --- /dev/null +++ b/biology/libsedml/Makefile @@ -0,0 +1,30 @@ +PORTNAME= libsedml +DISTVERSIONPREFIX= v +DISTVERSION= 2.0.26 +CATEGORIES= biology devel + +MAINTAINER= yuri@FreeBSD.org +COMMENT= C++ SED-ML library + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +BUILD_DEPENDS= libsbml>0:biology/libsbml \ + libnuml>0:biology/libnuml # statically linked, even into a shared library, see https://github.com/fbergmann/libSEDML/issues/155 +RUN_DEPENDS= libsbml>0:biology/libsbml \ + libnuml>0:biology/libnuml # when static lib libnuml.a is fixed these should be run-time dependency + +USES= cmake gnome +USE_GNOME= libxml2 +USE_LDCONFIG= yes + +USE_GITHUB= yes +GH_ACCOUNT= fbergmann +GH_PROJECT= libSEDML + +post-install: + @${RM} -r ${STAGEDIR}${DATADIR} + +# the project builds static libs with -fPIC, see https://github.com/fbergmann/libSEDML/issues/155 + +.include diff --git a/biology/libsedml/distinfo b/biology/libsedml/distinfo new file mode 100644 index 000000000000..305ade0a4d35 --- /dev/null +++ b/biology/libsedml/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1632069547 +SHA256 (fbergmann-libSEDML-v2.0.26_GH0.tar.gz) = 74334f2d2e0f4aae2f58f4013c432220ba12a6a6be4cf9478adbbefab7441b41 +SIZE (fbergmann-libSEDML-v2.0.26_GH0.tar.gz) = 956845 diff --git a/biology/libsedml/pkg-descr b/biology/libsedml/pkg-descr new file mode 100644 index 000000000000..5a7f83016d46 --- /dev/null +++ b/biology/libsedml/pkg-descr @@ -0,0 +1,4 @@ +The libSEDML project makes use of libSBML XML layer as well as code generation +as starting point to produce a library for reading and writing of SED-ML models. + +WWW: https://github.com/fbergmann/libSEDML diff --git a/biology/libsedml/pkg-plist b/biology/libsedml/pkg-plist new file mode 100644 index 000000000000..e88aa1bac57f --- /dev/null +++ b/biology/libsedml/pkg-plist @@ -0,0 +1,111 @@ +include/sedml/SedAbstractCurve.h +include/sedml/SedAbstractTask.h +include/sedml/SedAddXML.h +include/sedml/SedAdjustableParameter.h +include/sedml/SedAlgorithm.h +include/sedml/SedAlgorithmParameter.h +include/sedml/SedAnalysis.h +include/sedml/SedAppliedDimension.h +include/sedml/SedAxis.h +include/sedml/SedBase.h +include/sedml/SedBounds.h +include/sedml/SedChange.h +include/sedml/SedChangeAttribute.h +include/sedml/SedChangeXML.h +include/sedml/SedComputeChange.h +include/sedml/SedConstructorException.h +include/sedml/SedCurve.h +include/sedml/SedDataDescription.h +include/sedml/SedDataGenerator.h +include/sedml/SedDataRange.h +include/sedml/SedDataSet.h +include/sedml/SedDataSource.h +include/sedml/SedDocument.h +include/sedml/SedElementFilter.h +include/sedml/SedError.h +include/sedml/SedErrorLog.h +include/sedml/SedErrorTable.h +include/sedml/SedExperimentReference.h +include/sedml/SedFigure.h +include/sedml/SedFill.h +include/sedml/SedFitExperiment.h +include/sedml/SedFitMapping.h +include/sedml/SedFunctionalRange.h +include/sedml/SedLeastSquareObjectiveFunction.h +include/sedml/SedLine.h +include/sedml/SedListOf.h +include/sedml/SedListOfAdjustableParameters.h +include/sedml/SedListOfAlgorithmParameters.h +include/sedml/SedListOfAppliedDimensions.h +include/sedml/SedListOfChanges.h +include/sedml/SedListOfCurves.h +include/sedml/SedListOfDataDescriptions.h +include/sedml/SedListOfDataGenerators.h +include/sedml/SedListOfDataSets.h +include/sedml/SedListOfDataSources.h +include/sedml/SedListOfExperimentReferences.h +include/sedml/SedListOfFitExperiments.h +include/sedml/SedListOfFitMappings.h +include/sedml/SedListOfModels.h +include/sedml/SedListOfOutputs.h +include/sedml/SedListOfParameters.h +include/sedml/SedListOfRanges.h +include/sedml/SedListOfSetValues.h +include/sedml/SedListOfSimulations.h +include/sedml/SedListOfSlices.h +include/sedml/SedListOfStyles.h +include/sedml/SedListOfSubPlots.h +include/sedml/SedListOfSubTasks.h +include/sedml/SedListOfSurfaces.h +include/sedml/SedListOfTasks.h +include/sedml/SedListOfVariables.h +include/sedml/SedMarker.h +include/sedml/SedModel.h +include/sedml/SedNamespaces.h +include/sedml/SedObjective.h +include/sedml/SedOneStep.h +include/sedml/SedOutput.h +include/sedml/SedParameter.h +include/sedml/SedParameterEstimationReport.h +include/sedml/SedParameterEstimationResultPlot.h +include/sedml/SedParameterEstimationTask.h +include/sedml/SedPlot.h +include/sedml/SedPlot2D.h +include/sedml/SedPlot3D.h +include/sedml/SedRange.h +include/sedml/SedReader.h +include/sedml/SedRemoveXML.h +include/sedml/SedRepeatedTask.h +include/sedml/SedReport.h +include/sedml/SedSetValue.h +include/sedml/SedShadedArea.h +include/sedml/SedSimulation.h +include/sedml/SedSlice.h +include/sedml/SedSteadyState.h +include/sedml/SedStyle.h +include/sedml/SedSubPlot.h +include/sedml/SedSubTask.h +include/sedml/SedSurface.h +include/sedml/SedTask.h +include/sedml/SedTypeCodes.h +include/sedml/SedTypes.h +include/sedml/SedUniformRange.h +include/sedml/SedUniformTimeCourse.h +include/sedml/SedVariable.h +include/sedml/SedVectorRange.h +include/sedml/SedVisitor.h +include/sedml/SedWaterfallPlot.h +include/sedml/SedWriter.h +include/sedml/common/SedOperationReturnValues.h +include/sedml/common/SedmlEnumerations.h +include/sedml/common/common.h +include/sedml/common/extern.h +include/sedml/common/libsedml-config-common.h +include/sedml/common/libsedml-config.h +include/sedml/common/libsedml-namespace.h +include/sedml/common/libsedml-version.h +include/sedml/common/sedmlfwd.h +lib/libsedml-static.a +lib/libsedml.so +lib/libsedml.so.2 +lib/libsedml.so.2.0.26