diff --git a/biology/Makefile b/biology/Makefile index 02ba7b46b286..4e16a737f636 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,227 +1,228 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bamutil 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 += 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 += lamarc SUBDIR += libbigwig + SUBDIR += libgff SUBDIR += libgtextutils SUBDIR += libneurosim SUBDIR += libnuml SUBDIR += libsbml SUBDIR += libsedml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += mmseqs2 SUBDIR += molden SUBDIR += mopac 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-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-deeptools SUBDIR += py-deeptoolsintervals 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-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-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/libgff/Makefile b/biology/libgff/Makefile new file mode 100644 index 000000000000..6a16d0cd4557 --- /dev/null +++ b/biology/libgff/Makefile @@ -0,0 +1,16 @@ +PORTNAME= libgff +DISTVERSIONPREFIX= v +DISTVERSION= 2.0.0 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= GFF/GTF parsing library based on GCLib + +LICENSE= BSL +LICENSE_FILE= ${WRKSRC}/BoostLicense.txt + +USES= cmake +USE_GITHUB= yes +GH_ACCOUNT= COMBINE-lab + +.include diff --git a/biology/libgff/distinfo b/biology/libgff/distinfo new file mode 100644 index 000000000000..9bb01692e5c1 --- /dev/null +++ b/biology/libgff/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1631451501 +SHA256 (COMBINE-lab-libgff-v2.0.0_GH0.tar.gz) = 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c +SIZE (COMBINE-lab-libgff-v2.0.0_GH0.tar.gz) = 102152 diff --git a/biology/libgff/pkg-descr b/biology/libgff/pkg-descr new file mode 100644 index 000000000000..762881bedb74 --- /dev/null +++ b/biology/libgff/pkg-descr @@ -0,0 +1,11 @@ +This is an attempt to perform a simple "libraryfication" of the GFF/GTF +parsing code that is used in GFFRead codebase. There are not many +(any?) relatively lightweight GTF/GFF parsers exposing a C++ interface, +and the goal of this library is to provide this functionality without +the necessity of drawing in a heavy-weight dependency like SeqAn. Note: +This library draws directly from the code in GFFRead and GCLib, and +exists primarily to remove functionality (and hence code) that is +unnecessary for our downstream purposes. In the future, it may be +appropriate to just replace this library wholesale with GCLib. + +WWW: https://github.com/COMBINE-lab/libgff diff --git a/biology/libgff/pkg-plist b/biology/libgff/pkg-plist new file mode 100644 index 000000000000..474ea892d185 --- /dev/null +++ b/biology/libgff/pkg-plist @@ -0,0 +1,14 @@ +include/GArgs.h +include/GBase.h +include/GFaSeqGet.h +include/GFastaIndex.h +include/GHash.hh +include/GList.hh +include/GStr.h +include/GVec.hh +include/codons.h +include/gdna.h +include/gff.h +lib/libgff.a +lib/libgff/cmake/libgffConfig.cmake +lib/libgff/cmake/libgffConfigVersion.cmake