diff --git a/biology/Makefile b/biology/Makefile index e14218f00558..ba430926041c 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,220 +1,221 @@ 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 += libneurosim 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-libnuml SUBDIR += py-libsedml 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/libneurosim/Makefile b/biology/libneurosim/Makefile new file mode 100644 index 000000000000..9cdeb48e806b --- /dev/null +++ b/biology/libneurosim/Makefile @@ -0,0 +1,34 @@ +PORTNAME= libneurosim +DISTVERSIONPREFIX= v +DISTVERSION= 1.2.0 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Common interfaces for neuronal simulators + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +USES= autoreconf gmake libtool +USE_LDCONFIG= yes + +GNU_CONFIGURE= yes + +USE_GITHUB= yes +GH_ACCOUNT= INCF + +INSTALL_TARGET= install-strip + +BINARY_ALIAS= aclocal-1.15=aclocal automake-1.15=automake # workaround for the outdated aclocal-1.15 & automake-1.15 somehow placed into libltdl/Makefile + +OPTIONS_DEFINE= PYTHON +OPTIONS_DEFAULT= PYTHON +OPTIONS_SUB= yes + +PYTHON_CONFIGURE_ON= --with-python=${PYTHON_VER:R} +PYTHON_USES= python:3.6+ + +pre-build: # ignore failure of the first run of the build command that always fails first, see https://github.com/INCF/libneurosim/issues/21 + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} || ${TRUE} + +.include diff --git a/biology/libneurosim/distinfo b/biology/libneurosim/distinfo new file mode 100644 index 000000000000..697b456e39a0 --- /dev/null +++ b/biology/libneurosim/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1633636734 +SHA256 (INCF-libneurosim-v1.2.0_GH0.tar.gz) = 372fa0d8fb31950370f1d27bff4865e1200456239f4ea382c267d9a310175f83 +SIZE (INCF-libneurosim-v1.2.0_GH0.tar.gz) = 33695 diff --git a/biology/libneurosim/pkg-descr b/biology/libneurosim/pkg-descr new file mode 100644 index 000000000000..fecded8e27cd --- /dev/null +++ b/biology/libneurosim/pkg-descr @@ -0,0 +1,13 @@ +libneurosim is a general library that provides interfaces and common utility +code for neuronal simulators. + +Currently it provides the ConnectionGenerator interface. + +The ConnectionGenerator API is a standard interface supporting efficient +generation of network connectivity during model setup in neuronal network +simulators. It is intended as an abstraction isolating both sides of the API: +any simulator can use a given connection generator and a given simulator can use +any library providing the ConnectionGenerator interface. It was initially +developed to support the use of libcsa from NEST. + +WWW: https://github.com/INCF/libneurosim diff --git a/biology/libneurosim/pkg-plist b/biology/libneurosim/pkg-plist new file mode 100644 index 000000000000..5da69290ed22 --- /dev/null +++ b/biology/libneurosim/pkg-plist @@ -0,0 +1,13 @@ +include/neurosim/config.h +include/neurosim/connection_generator.h +include/neurosim/connection_generator_V2_0.h +%%PYTHON%%include/neurosim/pyneurosim.h +include/neurosim/version.h +lib/libneurosim.a +lib/libneurosim.so +lib/libneurosim.so.0 +lib/libneurosim.so.0.0.0 +%%PYTHON%%lib/libpy3neurosim.a +%%PYTHON%%lib/libpy3neurosim.so +%%PYTHON%%lib/libpy3neurosim.so.0 +%%PYTHON%%lib/libpy3neurosim.so.0.0.0