diff --git a/biology/Makefile b/biology/Makefile index 2ba55e0738ae..a4b704020908 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,235 +1,236 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis 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 += 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/barrnap/Makefile b/biology/barrnap/Makefile new file mode 100644 index 000000000000..90971ff06d7a --- /dev/null +++ b/biology/barrnap/Makefile @@ -0,0 +1,32 @@ +PORTNAME= barrnap +DISTVERSION= 0.9 +CATEGORIES= biology science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= BAsic Rapid Ribosomal RNA Predictor +WWW= https://github.com/tseemann/barrnap + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +RUN_DEPENDS= bedtools:biology/bedtools \ + nhmmer:biology/hmmer + +USES= gmake perl5 + +USE_GITHUB= yes +GH_ACCOUNT= tseemann + +NO_BUILD= yes +NO_ARCH= yes + +TEST_TARGET= test + +do-install: + ${INSTALL_SCRIPT} ${WRKSRC}/bin/barrnap ${STAGEDIR}${PREFIX}/bin + cd ${WRKSRC} && ${COPYTREE_SHARE} db ${STAGEDIR}${DATADIR} + ${REINPLACE_CMD} \ + -i '' -e 's|^my $$DBDIR = .*|my $$DBDIR = "${DATADIR}/db";|' \ + ${STAGEDIR}${PREFIX}/bin/barrnap + +.include diff --git a/biology/barrnap/distinfo b/biology/barrnap/distinfo new file mode 100644 index 000000000000..48b3f9e21728 --- /dev/null +++ b/biology/barrnap/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1669343398 +SHA256 (tseemann-barrnap-0.9_GH0.tar.gz) = 36c27cd4350531d98b3b2fb7d294a2d35c15b7365771476456d7873ba33cce15 +SIZE (tseemann-barrnap-0.9_GH0.tar.gz) = 11837541 diff --git a/biology/barrnap/pkg-descr b/biology/barrnap/pkg-descr new file mode 100644 index 000000000000..bec4ff368560 --- /dev/null +++ b/biology/barrnap/pkg-descr @@ -0,0 +1,6 @@ +SIMD-vectorized implementation of the Viterbi algorithm for profile HMM +alignment and introduced various other speed-ups. This accelerated HHsearch by a +factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is +~10x faster than PSI-BLAST and ~20x faster than HMMER3. Jobs to perform HHsearch +and HHblits searches with many query profile HMMs can be parallelized over cores +and over servers in a cluster using OpenMP and message passing interface (MPI). diff --git a/biology/barrnap/pkg-plist b/biology/barrnap/pkg-plist new file mode 100644 index 000000000000..fbf0ddaac319 --- /dev/null +++ b/biology/barrnap/pkg-plist @@ -0,0 +1,5 @@ +bin/barrnap +%%DATADIR%%/db/arc.hmm +%%DATADIR%%/db/bac.hmm +%%DATADIR%%/db/euk.hmm +%%DATADIR%%/db/mito.hmm