diff --git a/biology/Makefile b/biology/Makefile index 606e1982ee9b..adb71952bb1e 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,190 +1,191 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += bioparser SUBDIR += biosoup 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 += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps 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 += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit 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 += 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-bigwig SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio + SUBDIR += seqkit SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += spoa SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcf-split SUBDIR += vcf2hap SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include diff --git a/biology/seqkit/Makefile b/biology/seqkit/Makefile new file mode 100644 index 000000000000..4551cddb0836 --- /dev/null +++ b/biology/seqkit/Makefile @@ -0,0 +1,19 @@ +PORTNAME= seqkit +DISTVERSIONPREFIX= v +DISTVERSION= 0.16.0 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Cross-platform and ultrafast toolkit for FASTA/Q file manipulation + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= go:modules + +GO_MODULE= github.com/shenwei356/seqkit +GO_TARGET= ./${PORTNAME} + +PLIST_FILES= bin/${PORTNAME} + +.include diff --git a/biology/seqkit/distinfo b/biology/seqkit/distinfo new file mode 100644 index 000000000000..b24424ffad25 --- /dev/null +++ b/biology/seqkit/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1618605249 +SHA256 (go/biology_seqkit/seqkit-v0.16.0/v0.16.0.mod) = 2b29e40d7d4b891b1ece058363b9b4f8b3ba6385aa2855fb8d5f3df25bc83057 +SIZE (go/biology_seqkit/seqkit-v0.16.0/v0.16.0.mod) = 1211 +SHA256 (go/biology_seqkit/seqkit-v0.16.0/v0.16.0.zip) = 91fe05c0ead7b5dfafea7a0b3793583a3190befdcf3165735bf152182d0b0b11 +SIZE (go/biology_seqkit/seqkit-v0.16.0/v0.16.0.zip) = 29977829 diff --git a/biology/seqkit/pkg-descr b/biology/seqkit/pkg-descr new file mode 100644 index 000000000000..12fde7f0b3b6 --- /dev/null +++ b/biology/seqkit/pkg-descr @@ -0,0 +1,17 @@ +FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and +protein sequences. Common manipulations of FASTA/Q file include converting, +searching, filtering, deduplication, splitting, shuffling, and sampling. +Existing tools only implement some of these manipulations, and not particularly +efficiently, and some are only available for certain operating systems. +Furthermore, the complicated installation process of required packages and +running environments can render these programs less user friendly. + +SeqKit is a cross-platform ultrafast comprehensive toolkit for FASTA/Q +processing. SeqKit provides executable binary files for all major operating +systems, including Windows, Linux, and Mac OS X, and can be directly used +without any dependencies or pre-configurations. SeqKit demonstrates competitive +performance in execution time and memory usage compared to similar tools. The +efficiency and usability of SeqKit enable researchers to rapidly accomplish +common FASTA/Q file manipulations. + +WWW: https://github.com/shenwei356/seqkit