diff --git a/biology/Makefile b/biology/Makefile index fc30f158d16a..98b1f2663190 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,237 +1,238 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis 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 += 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-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-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 += 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/metaeuk/Makefile b/biology/metaeuk/Makefile new file mode 100644 index 000000000000..dd7010c29c00 --- /dev/null +++ b/biology/metaeuk/Makefile @@ -0,0 +1,31 @@ +PORTNAME= metaeuk +DISTVERSION= 6 +DISTVERSIONSUFFIX= -a5d39d9 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Gene discovery and annotation for large-scale eukaryotic metagenomics +WWW= https://github.com/soedinglab/metaeuk + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENCE.md + +BUILD_DEPENDS= xxd:editors/vim +TEST_DEPENDS= bash:shells/bash + +USES= cmake perl5 shebangfix +USE_PERL5= build + +USE_GITHUB= yes +GH_ACCOUNT= soedinglab +GH_TUPLE= soedinglab:metaeuk-regression:6404519:metaeuk_regression/tests \ + soedinglab:MMseqs2-Regression:f69b185:MMseqs2_Regression/lib/mmseqs/util/regression + +SHEBANG_GLOB= *.sh + +PLIST_FILES= bin/metaeuk + +do-test: + @cd ${WRKSRC}/tests && ./run.sh ${STAGEDIR}${PREFIX}/bin/metaeuk + +.include diff --git a/biology/metaeuk/distinfo b/biology/metaeuk/distinfo new file mode 100644 index 000000000000..cb642b65977d --- /dev/null +++ b/biology/metaeuk/distinfo @@ -0,0 +1,7 @@ +TIMESTAMP = 1669423980 +SHA256 (soedinglab-metaeuk-6-a5d39d9_GH0.tar.gz) = be19c26f5bdb7dcdd7bc48172105afecf19e5a2e5555edb3ba0c4aa0e4aac126 +SIZE (soedinglab-metaeuk-6-a5d39d9_GH0.tar.gz) = 13145257 +SHA256 (soedinglab-metaeuk-regression-6404519_GH0.tar.gz) = 5ac6c7438dc23374de5304564020e13ee7a6af99e60495083d74a5a272719b4d +SIZE (soedinglab-metaeuk-regression-6404519_GH0.tar.gz) = 6719192 +SHA256 (soedinglab-MMseqs2-Regression-f69b185_GH0.tar.gz) = 3774e16182cf8ce33d83c8c5170a57ebcec1ba137318d4762a89fd25c2890e78 +SIZE (soedinglab-MMseqs2-Regression-f69b185_GH0.tar.gz) = 27714150 diff --git a/biology/metaeuk/pkg-descr b/biology/metaeuk/pkg-descr new file mode 100644 index 000000000000..2ab6502d6c02 --- /dev/null +++ b/biology/metaeuk/pkg-descr @@ -0,0 +1,8 @@ +MetaEuk is a modular toolkit designed for large-scale gene discovery and +annotation in eukaryotic metagenomic contigs. MetaEuk combines the fast and +sensitive homology search capabilities of MMseqs2 with a dynamic programming +procedure to recover optimal exons sets. It reduces redundancies in multiple +discoveries of the same gene and resolves conflicting gene predictions on the +same strand. MetaEuk is GPLv3-licensed open source software that is implemented +in C++ and available for Linux and macOS. The software is designed to run +efficiently on multiple cores.