diff --git a/biology/Makefile b/biology/Makefile index 0c097ae77b3b..a99bb2d85c12 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,257 +1,258 @@ COMMENT = Biology SUBDIR += R-cran-Biobase SUBDIR += R-cran-BiocGenerics SUBDIR += R-cran-BiocManager SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += andi 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 += btllib 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 += fastani SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastq-trim SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fermi-lite SUBDIR += figtree SUBDIR += flash SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps SUBDIR += gffread SUBDIR += gkl 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 += 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-htseq SUBDIR += py-libnuml SUBDIR += py-libsedml SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-macs3 SUBDIR += py-mrcfile SUBDIR += py-multiqc SUBDIR += py-newick 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 += rna-seq SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += salmon SUBDIR += sam2pairwise SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqan3 SUBDIR += seqkit SUBDIR += seqtk SUBDIR += seqwish SUBDIR += sigviewer 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/fastani/Makefile b/biology/fastani/Makefile new file mode 100644 index 000000000000..5608f01a847f --- /dev/null +++ b/biology/fastani/Makefile @@ -0,0 +1,27 @@ +PORTNAME= fastani +DISTVERSIONPREFIX= v +DISTVERSION= 1.34 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Fast Whole-Genome Similarity (ANI) Estimation +WWW= https://github.com/shenwei356/unikmer/ + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libgsl.so:math/gsl + +USES= cmake:testing + +USE_GITHUB= yes +GH_ACCOUNT= ParBLiSS +GH_PROJECT= FastANI +GH_TUPLE= catchorg:Catch2:359542d:catch/ext/Catch2 + +CMAKE_OFF= BUILD_TESTING +CMAKE_TESTING_ON= BUILD_TESTING # 6 tests fail, see https://github.com/ParBLiSS/FastANI/issues/138 + +PLIST_FILES= bin/fastANI + +.include diff --git a/biology/fastani/distinfo b/biology/fastani/distinfo new file mode 100644 index 000000000000..d53b31741aa9 --- /dev/null +++ b/biology/fastani/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1726871246 +SHA256 (ParBLiSS-FastANI-v1.34_GH0.tar.gz) = dc185cf29b9fa40cdcc2c83bb48150db46835e49b9b64a3dbff8bc4d0f631cb1 +SIZE (ParBLiSS-FastANI-v1.34_GH0.tar.gz) = 3899028 +SHA256 (catchorg-Catch2-359542d_GH0.tar.gz) = 607bf5322291859a136b2580151f41897335e91c51fe0c4dd3950093ff96244b +SIZE (catchorg-Catch2-359542d_GH0.tar.gz) = 1031988 diff --git a/biology/fastani/files/patch-CMakeLists.txt b/biology/fastani/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..037ee9938029 --- /dev/null +++ b/biology/fastani/files/patch-CMakeLists.txt @@ -0,0 +1,12 @@ +--- CMakeLists.txt.orig 2023-07-28 20:41:45 UTC ++++ CMakeLists.txt +@@ -68,7 +68,8 @@ if(${BUILD_TESTING}) + Catch2::Catch2 Catch2::Catch2WithMain + ZLIB::ZLIB GSL::gsl GSL::gslcblas + ${OpenMP_CXX_LIBRARIES} +- gcov) ++ --coverage -g -O0 -fprofile-arcs -ftest-coverage ++ ) + catch_discover_tests(fastANITest) + file(COPY tests/data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + add_custom_target(lcov lcov -c -d .. -o fastANITest.out diff --git a/biology/fastani/files/patch-src_cgi_core__genome__identity.cpp b/biology/fastani/files/patch-src_cgi_core__genome__identity.cpp new file mode 100644 index 000000000000..050a0942eb2d --- /dev/null +++ b/biology/fastani/files/patch-src_cgi_core__genome__identity.cpp @@ -0,0 +1,11 @@ +--- src/cgi/core_genome_identity.cpp.orig 2024-09-20 22:30:43 UTC ++++ src/cgi/core_genome_identity.cpp +@@ -10,6 +10,8 @@ + #include + #include + ++#include ++ + //Own includes + #include "map/include/map_parameters.hpp" + #include "map/include/base_types.hpp" diff --git a/biology/fastani/pkg-descr b/biology/fastani/pkg-descr new file mode 100644 index 000000000000..78c6e5dbbf54 --- /dev/null +++ b/biology/fastani/pkg-descr @@ -0,0 +1,4 @@ +FastANI is developed for fast alignment-free computation of whole-genome Average +Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of +orthologous gene pairs shared between two microbial genomes. FastANI supports +pairwise comparison of both complete and draft genome assemblies.