diff --git a/biology/Makefile b/biology/Makefile index 3f12e044804a..35727e12139c 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,260 +1,261 @@ 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 += coverm 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 += mca-calling 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 += preseq 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/preseq/Makefile b/biology/preseq/Makefile new file mode 100644 index 000000000000..f25bd80cbe9d --- /dev/null +++ b/biology/preseq/Makefile @@ -0,0 +1,21 @@ +PORTNAME= preseq +DISTVERSION= 3.2.0 +CATEGORIES= biology +# Github-generated distfiles are incomplete +MASTER_SITES= https://github.com/smithlabcode/preseq/releases/download/v${DISTVERSION}/ + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Predict yield of distinct reads from a genomic library +WWW= https://github.com/smithlabcode/preseq + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libhts.so:biology/htslib + +USES= localbase + +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --enable-hts + +.include diff --git a/biology/preseq/distinfo b/biology/preseq/distinfo new file mode 100644 index 000000000000..6a9390f4dbc5 --- /dev/null +++ b/biology/preseq/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1732301093 +SHA256 (preseq-3.2.0.tar.gz) = 95b81c9054e0d651de398585c7e96b807ad98f0bdc541b3e46665febbe2134d9 +SIZE (preseq-3.2.0.tar.gz) = 6488708 diff --git a/biology/preseq/pkg-descr b/biology/preseq/pkg-descr new file mode 100644 index 000000000000..3e9357056178 --- /dev/null +++ b/biology/preseq/pkg-descr @@ -0,0 +1,5 @@ +The preseq package is aimed at predicting the yield of distinct reads +from a genomic library from an initial sequencing experiment. The +estimates can then be used to examine the utility of further +sequencing, optimize the sequencing depth, or to screen multiple +libraries to avoid low complexity samples. diff --git a/biology/preseq/pkg-plist b/biology/preseq/pkg-plist new file mode 100644 index 000000000000..b876eadc3daf --- /dev/null +++ b/biology/preseq/pkg-plist @@ -0,0 +1,17 @@ +bin/preseq +bin/to-mr +include/GenomicRegion.hpp +include/MappedRead.hpp +include/OptionParser.hpp +include/QualityScore.hpp +include/bisulfite_utils.hpp +include/chromosome_utils.hpp +include/cigar_utils.hpp +include/dna_four_bit.hpp +include/htslib_wrapper_deprecated.hpp +include/sam_record.hpp +include/sim_utils.hpp +include/smithlab_os.hpp +include/smithlab_utils.hpp +include/zlib_wrapper.hpp +lib/libsmithlab_cpp.a