diff --git a/biology/Makefile b/biology/Makefile index c8654fab2077..fe34cafefca7 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,246 +1,247 @@ 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 += 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/bifrost/Makefile b/biology/bifrost/Makefile new file mode 100644 index 000000000000..1ca58622a09a --- /dev/null +++ b/biology/bifrost/Makefile @@ -0,0 +1,18 @@ +PORTNAME= bifrost +DISTVERSIONPREFIX= v +DISTVERSION= 1.2.1 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Parallel construction, indexing and querying of de Bruijn graphs +WWW= https://github.com/pmelsted/bifrost + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= cmake +USE_GITHUB= yes + +GH_ACCOUNT= pmelsted + +.include diff --git a/biology/bifrost/distinfo b/biology/bifrost/distinfo new file mode 100644 index 000000000000..f92944f13d87 --- /dev/null +++ b/biology/bifrost/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1688397139 +SHA256 (pmelsted-bifrost-v1.2.1_GH0.tar.gz) = fe93080ef3ea71ff009fc206b5c17dd40fbfd18293000621a83d7d947dfedf1a +SIZE (pmelsted-bifrost-v1.2.1_GH0.tar.gz) = 905438 diff --git a/biology/bifrost/files/patch-src_strict__fstream.hpp b/biology/bifrost/files/patch-src_strict__fstream.hpp new file mode 100644 index 000000000000..e3b3caf35931 --- /dev/null +++ b/biology/bifrost/files/patch-src_strict__fstream.hpp @@ -0,0 +1,11 @@ +--- src/strict_fstream.hpp.orig 2023-07-03 15:14:36 UTC ++++ src/strict_fstream.hpp +@@ -64,7 +64,7 @@ static std::string strerror() + } else { + return "Unknown error (" + std::to_string(err_num) + ")"; + } +-#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__) ++#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__) || defined(__FreeBSD__) + // XSI-compliant strerror_r() + const int err_num = errno; // See above + if (strerror_r(err_num, buff.data(), buff.size()) == 0) { diff --git a/biology/bifrost/pkg-descr b/biology/bifrost/pkg-descr new file mode 100644 index 000000000000..68c41b2f44fc --- /dev/null +++ b/biology/bifrost/pkg-descr @@ -0,0 +1,3 @@ +Bifrost is a tool and API for parallel construction, indexing and +querying of colored and compacted de Bruijn graphs from FASTA/FASTQ +DNA/RNA sequence files. diff --git a/biology/bifrost/pkg-plist b/biology/bifrost/pkg-plist new file mode 100644 index 000000000000..7d555618743c --- /dev/null +++ b/biology/bifrost/pkg-plist @@ -0,0 +1,53 @@ +bin/Bifrost +include/bifrost/BitContainer.hpp +include/bifrost/BlockedBloomFilter.hpp +include/bifrost/ColorSet.hpp +include/bifrost/ColoredCDBG.hpp +include/bifrost/ColoredCDBG.tcc +include/bifrost/Common.hpp +include/bifrost/CompactedDBG.hpp +include/bifrost/CompactedDBG.tcc +include/bifrost/CompressedCoverage.hpp +include/bifrost/CompressedSequence.hpp +include/bifrost/DataAccessor.hpp +include/bifrost/DataAccessor.tcc +include/bifrost/DataManager.hpp +include/bifrost/DataStorage.hpp +include/bifrost/DataStorage.tcc +include/bifrost/FASTX_Parser.hpp +include/bifrost/File_Parser.hpp +include/bifrost/GFA_Parser.hpp +include/bifrost/IO.tcc +include/bifrost/Kmer.hpp +include/bifrost/KmerCovIndex.hpp +include/bifrost/KmerCovIndex.tcc +include/bifrost/KmerHashTable.hpp +include/bifrost/KmerIterator.hpp +include/bifrost/KmerStream.hpp +include/bifrost/Lock.hpp +include/bifrost/MinimizerIndex.hpp +include/bifrost/NeighborIterator.hpp +include/bifrost/NeighborIterator.tcc +include/bifrost/RepHash.hpp +include/bifrost/Search.tcc +include/bifrost/StreamCounter.hpp +include/bifrost/TinyBitmap.hpp +include/bifrost/TinyVector.hpp +include/bifrost/Unitig.hpp +include/bifrost/UnitigIterator.hpp +include/bifrost/UnitigIterator.tcc +include/bifrost/UnitigMap.hpp +include/bifrost/UnitigMap.tcc +include/bifrost/getRSS.h +include/bifrost/kseq.h +include/bifrost/libdivide.h +include/bifrost/libpopcnt.h +include/bifrost/minHashIterator.hpp +include/bifrost/roaring.h +include/bifrost/roaring.hh +include/bifrost/rw_spin_lock.h +include/bifrost/strict_fstream.hpp +include/bifrost/wyhash.h +include/bifrost/zstr.hpp +lib/libbifrost.a +lib/libbifrost.so