diff --git a/biology/Makefile b/biology/Makefile index 1c570b26ebb9..25ed50f54925 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,233 +1,234 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bamutil SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bfc SUBDIR += bio-mocha 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 += fastq-trim 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 += gffread 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 += kmcp SUBDIR += lamarc SUBDIR += libbigwig + SUBDIR += libcombine SUBDIR += libgff SUBDIR += libgtextutils SUBDIR += libneurosim SUBDIR += libnuml SUBDIR += libsbml SUBDIR += libsedml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += mmseqs2 SUBDIR += molden 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-bcbio-gff SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-deeptools SUBDIR += py-deeptoolsintervals SUBDIR += py-dna-features-viewer SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-goatools SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-libnuml SUBDIR += py-libsedml SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-mrcfile SUBDIR += py-multiqc SUBDIR += py-ont-fast5-api SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-py2bit SUBDIR += py-pybigwig SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-python-libsbml SUBDIR += py-pywgsim SUBDIR += py-resdk SUBDIR += py-scikit-bio SUBDIR += py-valerius 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/libcombine/Makefile b/biology/libcombine/Makefile new file mode 100644 index 000000000000..888059b5caad --- /dev/null +++ b/biology/libcombine/Makefile @@ -0,0 +1,30 @@ +PORTNAME= libcombine +DISTVERSIONPREFIX= v +DISTVERSION= 0.2.19 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= C++ library for working with the COMBINE archive format +WWW= https://sbml.org/software/libsbml/ + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.md + +LIB_DEPENDS= libsbml.so:biology/libsbml + +USES= cmake:testing gnome localbase:ldflags +USE_GNOME= libxml2 +USE_LDCONFIG= yes + +USE_GITHUB= yes +GH_ACCOUNT= sbmlteam +GH_PROJECT= libCombine +GH_TUPLE= fbergmann:zipper:6f54c03:zipper/src/zipper \ + sebastiandev:minizip:e3a8cb7:zipper_minizip/src/zipper/minizip + +CMAKE_OFF= BUILD_TEST +CMAKE_TESTING_ON= BUILD_TEST # tests fail to build, see https://github.com/sbmlteam/libCombine/issues/58 + +LDFLAGS+= -lsbml # FindSBML.cmake fails to set this link flag + +.include diff --git a/biology/libcombine/distinfo b/biology/libcombine/distinfo new file mode 100644 index 000000000000..935e8183950b --- /dev/null +++ b/biology/libcombine/distinfo @@ -0,0 +1,7 @@ +TIMESTAMP = 1666331339 +SHA256 (sbmlteam-libCombine-v0.2.19_GH0.tar.gz) = a9ac562cca70cd8862b3f3cd65c98e8e455896732a8e1d3ee1ff32bf8ec02ac5 +SIZE (sbmlteam-libCombine-v0.2.19_GH0.tar.gz) = 1524012 +SHA256 (fbergmann-zipper-6f54c03_GH0.tar.gz) = 61aba13ecc2cb23617cf6496bc67739820a7b8c203b3dbb0ce9fddd0a68598d6 +SIZE (fbergmann-zipper-6f54c03_GH0.tar.gz) = 124726 +SHA256 (sebastiandev-minizip-e3a8cb7_GH0.tar.gz) = 14492faf0694bf075312626ffba0fe6fcfccb450001db5b01fece2134d69a75d +SIZE (sebastiandev-minizip-e3a8cb7_GH0.tar.gz) = 85593 diff --git a/biology/libcombine/files/patch-CMakeModules_FindLIBSBML.cmake b/biology/libcombine/files/patch-CMakeModules_FindLIBSBML.cmake new file mode 100644 index 000000000000..c7d6e386f2c3 --- /dev/null +++ b/biology/libcombine/files/patch-CMakeModules_FindLIBSBML.cmake @@ -0,0 +1,23 @@ +--- CMakeModules/FindLIBSBML.cmake.orig 2022-10-21 06:11:59 UTC ++++ CMakeModules/FindLIBSBML.cmake +@@ -124,9 +124,7 @@ endif (NOT LIBSBML_INCLUDE_DIR) + + + find_library(LIBSBML_LIBRARY +- NAMES sbml-static +- sbml +- libsbml-static ++ NAMES sbml + libsbml + PATHS $ENV{LIBSBML_DIR}/lib + $ENV{LIBSBML_DIR} +@@ -144,8 +142,7 @@ find_library(LIBSBML_LIBRARY + + if (NOT LIBSBML_LIBRARY) + find_library(LIBSBML_LIBRARY +- NAMES sbml-static +- sbml) ++ NAMES sbml) + endif (NOT LIBSBML_LIBRARY) + + if (NOT LIBSBML_LIBRARY) diff --git a/biology/libcombine/files/patch-dev_generated_CMakeLists.txt b/biology/libcombine/files/patch-dev_generated_CMakeLists.txt new file mode 100644 index 000000000000..5907bbf5a841 --- /dev/null +++ b/biology/libcombine/files/patch-dev_generated_CMakeLists.txt @@ -0,0 +1,11 @@ +--- dev/generated/CMakeLists.txt.orig 2022-10-21 06:12:43 UTC ++++ dev/generated/CMakeLists.txt +@@ -221,7 +221,7 @@ endif(WITH_SWIG) + # Locate libsbml + # + find_library(LIBSBML_LIBRARY +- NAMES libsbml-static.lib sbml-static libsbml.lib sbml ++ NAMES libsbml.lib sbml + PATHS ${LIBCOMBINE_DEPENDENCY_DIR}/lib + /usr/local/lib + /usr/lib diff --git a/biology/libcombine/pkg-descr b/biology/libcombine/pkg-descr new file mode 100644 index 000000000000..6cee46bab321 --- /dev/null +++ b/biology/libcombine/pkg-descr @@ -0,0 +1,4 @@ +LibCombine implements a C++ API library providing support for the Combine +Archive. The library is written after the likeness of libSBML (and in fact some +classes have been generated using DEVISER). Thus even thought he core is +written in C++, the classes can be accessed via SWIG from .NET, Java and Python. diff --git a/biology/libcombine/pkg-plist b/biology/libcombine/pkg-plist new file mode 100644 index 000000000000..d453477f9f49 --- /dev/null +++ b/biology/libcombine/pkg-plist @@ -0,0 +1,43 @@ +include/combine/combinearchive.h +include/combine/knownformats.h +include/combine/omexdescription.h +include/combine/util.h +include/combine/vcard.h +include/omex/CaBase.h +include/omex/CaConstructorException.h +include/omex/CaContent.h +include/omex/CaCrossRef.h +include/omex/CaError.h +include/omex/CaErrorLog.h +include/omex/CaErrorTable.h +include/omex/CaListOf.h +include/omex/CaListOfContents.h +include/omex/CaListOfCrossRefs.h +include/omex/CaNamespaces.h +include/omex/CaOmexManifest.h +include/omex/CaReader.h +include/omex/CaTypeCodes.h +include/omex/CaTypes.h +include/omex/CaVisitor.h +include/omex/CaWriter.h +include/omex/common/CaOperationReturnValues.h +include/omex/common/combinefwd.h +include/omex/common/common.h +include/omex/common/extern.h +include/omex/common/libcombine-config-common.h +include/omex/common/libcombine-config.h +include/omex/common/libcombine-namespace.h +include/omex/common/libcombine-version.h +lib/cmake/Combine-config-version.cmake +lib/cmake/Combine-config.cmake +lib/cmake/Combine-static-config-version.cmake +lib/cmake/Combine-static-config.cmake +lib/cmake/Combine-static-targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/Combine-static-targets.cmake +lib/cmake/Combine-targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/Combine-targets.cmake +lib/libCombine-static.a +lib/libCombine.so +lib/libCombine.so.0 +lib/libCombine.so.0.2.19 +share/cmake/Modules/FindLIBCOMBINE.cmake