diff --git a/biology/Makefile b/biology/Makefile index 801bff937770..43439e1f4a89 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,243 +1,244 @@ 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 += 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 += 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 += mafft SUBDIR += mapm3 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/wfa2-lib/Makefile b/biology/wfa2-lib/Makefile new file mode 100644 index 000000000000..cb334b9bf0c3 --- /dev/null +++ b/biology/wfa2-lib/Makefile @@ -0,0 +1,20 @@ +PORTNAME= wfa2-lib +DISTVERSIONPREFIX= v +DISTVERSION= 2.3.2 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Exact gap-affine algorithm using homology to accelerate alignment +WWW= https://github.com/smarco/WFA2-lib + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= cmake pkgconfig +USE_GITHUB= yes +USE_LDCONFIG= yes + +GH_ACCOUNT= smarco +GH_PROJECT= WFA2-lib + +.include diff --git a/biology/wfa2-lib/distinfo b/biology/wfa2-lib/distinfo new file mode 100644 index 000000000000..09a5d3555324 --- /dev/null +++ b/biology/wfa2-lib/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1675088499 +SHA256 (smarco-WFA2-lib-v2.3.2_GH0.tar.gz) = 310e3886506ab57d04205cdf5fed3ef31969ce39e9c6d341fd5c8a0d4aa0830b +SIZE (smarco-WFA2-lib-v2.3.2_GH0.tar.gz) = 4150874 diff --git a/biology/wfa2-lib/files/patch-system_profiler__timer.h b/biology/wfa2-lib/files/patch-system_profiler__timer.h new file mode 100644 index 000000000000..5ebce4ad2b2e --- /dev/null +++ b/biology/wfa2-lib/files/patch-system_profiler__timer.h @@ -0,0 +1,10 @@ +--- system/profiler_timer.h.orig 2023-01-30 14:47:11 UTC ++++ system/profiler_timer.h +@@ -33,6 +33,7 @@ + #ifndef PROFILER_TIMER_H + #define PROFILER_TIMER_H + ++#include // Required on FreeBSD 12.3 + #include "profiler_counter.h" + + /* diff --git a/biology/wfa2-lib/pkg-descr b/biology/wfa2-lib/pkg-descr new file mode 100644 index 000000000000..24a0b82a109e --- /dev/null +++ b/biology/wfa2-lib/pkg-descr @@ -0,0 +1,9 @@ +The wavefront alignment (WFA) algorithm is an exact gap-affine +algorithm that takes advantage of homologous regions between the +sequences to accelerate the alignment process. Unlike traditional +dynamic programming algorithms that run in quadratic time, the WFA runs +in time O(ns+s^2), proportional to the sequence length n and the +alignment score s, using O(s^2) memory (or O(s) using the +ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple +computational patterns that the modern compilers can automatically +vectorize for different architectures without adapting the code. diff --git a/biology/wfa2-lib/pkg-plist b/biology/wfa2-lib/pkg-plist new file mode 100644 index 000000000000..235ff54015ca --- /dev/null +++ b/biology/wfa2-lib/pkg-plist @@ -0,0 +1,46 @@ +include/wfa2lib/alignment/affine2p_penalties.h +include/wfa2lib/alignment/affine_penalties.h +include/wfa2lib/alignment/cigar.h +include/wfa2lib/alignment/linear_penalties.h +include/wfa2lib/alignment/score_matrix.h +include/wfa2lib/system/mm_allocator.h +include/wfa2lib/system/mm_stack.h +include/wfa2lib/system/profiler_counter.h +include/wfa2lib/system/profiler_timer.h +include/wfa2lib/utils/bitmap.h +include/wfa2lib/utils/commons.h +include/wfa2lib/utils/dna_text.h +include/wfa2lib/utils/heatmap.h +include/wfa2lib/utils/sequence_buffer.h +include/wfa2lib/utils/string_padded.h +include/wfa2lib/utils/vector.h +include/wfa2lib/wavefront/wavefront.h +include/wfa2lib/wavefront/wavefront_align.h +include/wfa2lib/wavefront/wavefront_aligner.h +include/wfa2lib/wavefront/wavefront_attributes.h +include/wfa2lib/wavefront/wavefront_backtrace.h +include/wfa2lib/wavefront/wavefront_backtrace_buffer.h +include/wfa2lib/wavefront/wavefront_backtrace_offload.h +include/wfa2lib/wavefront/wavefront_bialign.h +include/wfa2lib/wavefront/wavefront_bialigner.h +include/wfa2lib/wavefront/wavefront_components.h +include/wfa2lib/wavefront/wavefront_compute.h +include/wfa2lib/wavefront/wavefront_compute_affine.h +include/wfa2lib/wavefront/wavefront_compute_affine2p.h +include/wfa2lib/wavefront/wavefront_compute_edit.h +include/wfa2lib/wavefront/wavefront_compute_linear.h +include/wfa2lib/wavefront/wavefront_debug.h +include/wfa2lib/wavefront/wavefront_display.h +include/wfa2lib/wavefront/wavefront_extend.h +include/wfa2lib/wavefront/wavefront_heuristic.h +include/wfa2lib/wavefront/wavefront_offset.h +include/wfa2lib/wavefront/wavefront_pcigar.h +include/wfa2lib/wavefront/wavefront_penalties.h +include/wfa2lib/wavefront/wavefront_plot.h +include/wfa2lib/wavefront/wavefront_slab.h +include/wfa2lib/wavefront/wavefront_unialign.h +include/wfa2lib/wavefront/wfa.h +include/wfa2lib/wavefront/wfa.hpp +lib/libwfa2.a +lib/libwfa2.so +lib/libwfa2.so.0