diff --git a/biology/Makefile b/biology/Makefile index e24861f2a317..ec370d664a52 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,217 +1,218 @@ 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-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/py-libnuml/Makefile b/biology/py-libnuml/Makefile new file mode 100644 index 000000000000..dcd1b9df3d08 --- /dev/null +++ b/biology/py-libnuml/Makefile @@ -0,0 +1,31 @@ +PORTNAME= libnuml +DISTVERSIONPREFIX= v +DISTVERSION= 1.1.4 +CATEGORIES= biology devel +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Numerical Markup Language for Python + +LICENSE= LGPL21 + +BUILD_DEPENDS= swig:devel/swig +LIB_DEPENDS= libnuml.so:biology/libnuml + +USES= cmake localbase:ldflags python +USE_PYTHON= flavors + +USE_GITHUB= yes +GH_ACCOUNT= NuML +GH_PROJECT= NuML + +WKSRC_SUBDIR= ${PORTNAME}/src/bindings/python + +CMAKE_ARGS= -DCMAKE_INSTALL_LIBDIR=lib + +LDFLAGS+= -lnuml # otherwise it builds a broken shared object, see https://github.com/NuML/NuML/issues/21 + +post-extract: + @${RLN} ${WRKSRC}/../../../VERSION.txt ${WRKSRC}/VERSION.txt + +.include diff --git a/biology/py-libnuml/distinfo b/biology/py-libnuml/distinfo new file mode 100644 index 000000000000..6d10a1bca0ea --- /dev/null +++ b/biology/py-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/py-libnuml/files/patch-CMakeLists.txt b/biology/py-libnuml/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..12167a58575d --- /dev/null +++ b/biology/py-libnuml/files/patch-CMakeLists.txt @@ -0,0 +1,22 @@ +--- CMakeLists.txt.orig 2021-04-29 08:24:05 UTC ++++ CMakeLists.txt +@@ -62,6 +62,7 @@ ADD_CUSTOM_COMMAND( + OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libnuml_wrap.cpp + COMMAND "${SWIG_EXECUTABLE}" + ARGS -I${CMAKE_CURRENT_SOURCE_DIR}/../swig/ ++ -I${CMAKE_INSTALL_PREFIX}/include + -I${CMAKE_SOURCE_DIR}/ + -I${CMAKE_BINARY_DIR}/ + -I${CMAKE_BINARY_DIR}/src +@@ -142,9 +143,9 @@ if (PYTHON_USE_DYNAMIC_LOOKUP) + if (APPLE) + set_target_properties (binding_python_lib PROPERTIES LINK_FLAGS "-undefined dynamic_lookup") + endif() +- target_link_libraries(binding_python_lib ${LIBNUML_LIBRARY}-static) ++ target_link_libraries(binding_python_lib ${LIBNUML_LIBRARY}) + else() +- target_link_libraries(binding_python_lib ${LIBNUML_LIBRARY}-static ${PYTHON_LIBRARIES}) ++ target_link_libraries(binding_python_lib ${LIBNUML_LIBRARY} ${PYTHON_LIBRARIES}) + endif() + + diff --git a/biology/py-libnuml/pkg-descr b/biology/py-libnuml/pkg-descr new file mode 100644 index 000000000000..a8a267cc7f76 --- /dev/null +++ b/biology/py-libnuml/pkg-descr @@ -0,0 +1,8 @@ +This is a Python binding for libnuml, the Numerical Markup Language library. + +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/py-libnuml/pkg-plist b/biology/py-libnuml/pkg-plist new file mode 100644 index 000000000000..8156ea3a6416 --- /dev/null +++ b/biology/py-libnuml/pkg-plist @@ -0,0 +1,3 @@ +%%PYTHON_SITELIBDIR%%/libnuml.pth +%%PYTHON_SITELIBDIR%%/libnuml/_libnuml.so +%%PYTHON_SITELIBDIR%%/libnuml/libnuml.py