diff --git a/biology/Makefile b/biology/Makefile index 71d625b98e9f..e41e9edcb828 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,248 +1,249 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += atac-seq SUBDIR += augustus SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bamutil SUBDIR += barrnap SUBDIR += bbmap SUBDIR += bcf-score SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bfc SUBDIR += bifrost 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 += chip-seq 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 += fasda 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 += locarna SUBDIR += mafft SUBDIR += mapm3 SUBDIR += mashmap SUBDIR += megahit SUBDIR += metaeuk 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-biosig 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-pyrodigal 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 += rna-seq 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 += wfa2-lib SUBDIR += wise .include diff --git a/biology/locarna/Makefile b/biology/locarna/Makefile new file mode 100644 index 000000000000..6c6c008b2384 --- /dev/null +++ b/biology/locarna/Makefile @@ -0,0 +1,28 @@ +PORTNAME= locarna +DISTVERSION= 2.0.0 +CATEGORIES= biology +MASTER_SITES= https://github.com/s-will/LocARNA/releases/download/v${DISTVERSION}/ + +MAINTAINER= yuri@FreeBSD.org +COMMENT= LocARNA provides several tools for the structural analysis of RNA +WWW= https://github.com/s-will/LocARNA + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +BUILD_DEPENDS= ${LOCALBASE}/lib/libRNA.a:biology/viennarna +LIB_DEPENDS= libgmp.so:math/gmp \ + libgsl.so:math/gsl \ + libmpfr.so:math/mpfr + +USES= autoreconf gmake libtool perl5 pkgconfig shebangfix +USE_LDCONFIG= yes + +SHEBANG_FILES= src/Utils/locarna_mcc + +GNU_CONFIGURE= yes + +INSTALL_TARGET= install-strip +TEST_TARGET= check # tests fail to compile, see https://github.com/s-will/LocARNA/issues/80 + +.include diff --git a/biology/locarna/distinfo b/biology/locarna/distinfo new file mode 100644 index 000000000000..1b872dee9ea6 --- /dev/null +++ b/biology/locarna/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1689540878 +SHA256 (locarna-2.0.0.tar.gz) = 3be0d2cac7f7451f8b741983e22803b546de2074d837b425fb1b69ccc718ebbc +SIZE (locarna-2.0.0.tar.gz) = 3049455 diff --git a/biology/locarna/pkg-descr b/biology/locarna/pkg-descr new file mode 100644 index 000000000000..dd5376f2a390 --- /dev/null +++ b/biology/locarna/pkg-descr @@ -0,0 +1,13 @@ +LocARNA is a collection of alignment tools for the structural analysis of RNA. +Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common +structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment +and is in particular suited for analyzing sets of related RNAs without known +common structure. + +LocARNA distinguishes itself from many other Sankoff-style multiple alignment +programs by its performance and low memory complexity, high accuracy, and +richness of features. As unique features, it offers structure-local alignment, +flexible structure and anchor constraints, and provides efficient computation of +reliabilities in sequence-structure alignment. The package offers a robust core +of features and is used as experimental platform for the incorporation of new +features in RNA sequence-structure alignment. diff --git a/biology/locarna/pkg-plist b/biology/locarna/pkg-plist new file mode 100644 index 000000000000..0d6039099397 --- /dev/null +++ b/biology/locarna/pkg-plist @@ -0,0 +1,134 @@ +bin/LocARNA_RNAz.pm +bin/RNAz.pm +bin/aln-seqs.pl +bin/aln2fa.pl +bin/alnsel.pl +bin/average-dot.pl +bin/benchmark-plot.R +bin/dot2pp +bin/exparna_p +bin/exploc_p +bin/gen-reliab-dot.pl +bin/locarna +bin/locarna-mea.pl +bin/locarna-motif-scan +bin/locarna_deviation +bin/locarna_mcc +bin/locarna_p +bin/locarna_rnafold_pp +bin/locarnap-predict-and-plot.pl +bin/locarnap-realign-all.pl +bin/locarnap-revcomp.pl +bin/locarnap-revisit-RNAz-hits.pl +bin/locarnap_fit +bin/locarnate +bin/mlocarna +bin/mlocarna_nnames +bin/plot-bmprobs +bin/pp2dot +bin/reliability-profile.pl +bin/ribosum2cc +bin/sparse +include/LocARNA-2.0/LocARNA/aligner.hh +include/LocARNA-2.0/LocARNA/aligner_impl.hh +include/LocARNA-2.0/LocARNA/aligner_n.hh +include/LocARNA-2.0/LocARNA/aligner_p.hh +include/LocARNA-2.0/LocARNA/aligner_p.icc +include/LocARNA-2.0/LocARNA/aligner_params.hh +include/LocARNA-2.0/LocARNA/aligner_restriction.hh +include/LocARNA-2.0/LocARNA/alignment.hh +include/LocARNA-2.0/LocARNA/alignment_impl.hh +include/LocARNA-2.0/LocARNA/alphabet.hh +include/LocARNA-2.0/LocARNA/alphabet.icc +include/LocARNA-2.0/LocARNA/anchor_constraints.hh +include/LocARNA-2.0/LocARNA/arc_matches.hh +include/LocARNA-2.0/LocARNA/aux.hh +include/LocARNA-2.0/LocARNA/base_pair_filter.hh +include/LocARNA-2.0/LocARNA/basepairs.hh +include/LocARNA-2.0/LocARNA/confusion_matrix.hh +include/LocARNA-2.0/LocARNA/discrete_distribution.hh +include/LocARNA-2.0/LocARNA/edge_probs.hh +include/LocARNA-2.0/LocARNA/edge_probs.icc +include/LocARNA-2.0/LocARNA/exact_matcher.hh +include/LocARNA-2.0/LocARNA/ext_rna_data.hh +include/LocARNA-2.0/LocARNA/ext_rna_data_impl.hh +include/LocARNA-2.0/LocARNA/free_endgaps.hh +include/LocARNA-2.0/LocARNA/global_stopwatch.hh +include/LocARNA-2.0/LocARNA/infty_int.hh +include/LocARNA-2.0/LocARNA/main_helper.icc +include/LocARNA-2.0/LocARNA/matrices.hh +include/LocARNA-2.0/LocARNA/matrix.hh +include/LocARNA-2.0/LocARNA/mcc_matrices.hh +include/LocARNA-2.0/LocARNA/multiple_alignment.hh +include/LocARNA-2.0/LocARNA/named_arguments.hh +include/LocARNA-2.0/LocARNA/options.hh +include/LocARNA-2.0/LocARNA/pfold_params.hh +include/LocARNA-2.0/LocARNA/quadmath.hh +include/LocARNA-2.0/LocARNA/ribofit.hh +include/LocARNA-2.0/LocARNA/ribofit_will2014.icc +include/LocARNA-2.0/LocARNA/ribofit_will2014.ihh +include/LocARNA-2.0/LocARNA/ribosum.hh +include/LocARNA-2.0/LocARNA/ribosum85_60.icc +include/LocARNA-2.0/LocARNA/rna_data.hh +include/LocARNA-2.0/LocARNA/rna_data_impl.hh +include/LocARNA-2.0/LocARNA/rna_ensemble.hh +include/LocARNA-2.0/LocARNA/rna_ensemble_impl.hh +include/LocARNA-2.0/LocARNA/rna_structure.hh +include/LocARNA-2.0/LocARNA/scoring.hh +include/LocARNA-2.0/LocARNA/scoring_fwd.hh +include/LocARNA-2.0/LocARNA/sequence.hh +include/LocARNA-2.0/LocARNA/sequence_annotation.hh +include/LocARNA-2.0/LocARNA/sparse_matrix.hh +include/LocARNA-2.0/LocARNA/sparse_vector.hh +include/LocARNA-2.0/LocARNA/sparse_vector_base.hh +include/LocARNA-2.0/LocARNA/sparsification_mapper.hh +include/LocARNA-2.0/LocARNA/std_help_text.ihh +include/LocARNA-2.0/LocARNA/stopwatch.hh +include/LocARNA-2.0/LocARNA/stral_score.hh +include/LocARNA-2.0/LocARNA/string1.hh +include/LocARNA-2.0/LocARNA/trace_controller.hh +include/LocARNA-2.0/LocARNA/tuples.hh +include/LocARNA-2.0/LocARNA/zip.hh +lib/libLocARNA-2.0.a +lib/libLocARNA-2.0.so +lib/libLocARNA-2.0.so.1 +lib/libLocARNA-2.0.so.1.0.4 +lib/perl/MLocarna.pm +lib/perl/MLocarna/Aux.pm +lib/perl/MLocarna/MatchProbs.pm +lib/perl/MLocarna/NameNormalizer.pm +lib/perl/MLocarna/PairwiseAligners.pm +lib/perl/MLocarna/SparseMatrix.pm +lib/perl/MLocarna/Tree.pm +lib/perl/MLocarna/threaded.pm +lib/perl/MLocarna/unthreaded.pm +libdata/pkgconfig/LocARNA-2.0.pc +man/man1/aln-seqs.pl.1.gz +man/man1/aln2fa.pl.1.gz +man/man1/alnsel.pl.1.gz +man/man1/average-dot.pl.1.gz +man/man1/dot2pp.1.gz +man/man1/exparna_p.1.gz +man/man1/exploc_p.1.gz +man/man1/gen-reliab-dot.pl.1.gz +man/man1/locarna-mea.pl.1.gz +man/man1/locarna-motif-scan.1.gz +man/man1/locarna.1.gz +man/man1/locarna_deviation.1.gz +man/man1/locarna_mcc.1.gz +man/man1/locarna_p.1.gz +man/man1/locarna_rnafold_pp.1.gz +man/man1/locarnap-predict-and-plot.pl.1.gz +man/man1/locarnap-realign-all.pl.1.gz +man/man1/locarnap-revcomp.pl.1.gz +man/man1/locarnap-revisit-RNAz-hits.pl.1.gz +man/man1/locarnap_fit.1.gz +man/man1/locarnate.1.gz +man/man1/mlocarna.1.gz +man/man1/mlocarna_nnames.1.gz +man/man1/plot-bmprobs.1.gz +man/man1/pp2dot.1.gz +man/man1/reliability-profile.pl.1.gz +man/man1/ribosum2cc.1.gz +man/man1/sparse.1.gz +%%DATADIR%%/Matrices/RIBOSUM85_60