diff --git a/biology/Makefile b/biology/Makefile index 2a6da67d4b30..faa2b7ac520f 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,254 +1,255 @@ COMMENT = Biology SUBDIR += R-cran-Biobase SUBDIR += R-cran-BiocGenerics SUBDIR += R-cran-BiocManager SUBDIR += abyss SUBDIR += ad2vcf 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 += 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 += 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 += 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 += 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 += 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/fermi-lite/Makefile b/biology/fermi-lite/Makefile new file mode 100644 index 000000000000..86512a27552a --- /dev/null +++ b/biology/fermi-lite/Makefile @@ -0,0 +1,39 @@ +PORTNAME= fermi-lite +DISTVERSIONPREFIX= v +DISTVERSION= 0.1-13 +DISTVERSIONSUFFIX= -g85f159e +CATEGORIES= biology devel + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Library and tool for assembling Illumina short reads in small regions +WWW= https://github.com/lh3/fermi-lite + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +USES= gmake +USE_LDCONFIG= yes + +USE_GITHUB= yes +GH_ACCOUNT= lh3 + +MAKE_ARGS= CFLAGS="${CFLAGS}" + +BINARY_ALIAS= gcc=${CC} + +PLIST_FILES= bin/fml-asm \ + include/fml.h \ + lib/libfml.a \ + lib/libfml.so + +post-build: + @cd ${WRKSRC} && \ + ${CC} ${CFLAGS} -fPIC ${LDFLAGS} -shared $$(ls *.c | grep -v example.c) -o libfml.so + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/fml-asm ${STAGEDIR}${PREFIX}/bin + ${INSTALL_DATA} ${WRKSRC}/fml.h ${STAGEDIR}${PREFIX}/include + ${INSTALL_DATA} ${WRKSRC}/libfml.a ${STAGEDIR}${PREFIX}/lib + ${INSTALL_LIB} ${WRKSRC}/libfml.so ${STAGEDIR}${PREFIX}/lib + +.include diff --git a/biology/fermi-lite/distinfo b/biology/fermi-lite/distinfo new file mode 100644 index 000000000000..a2bcd5b34a70 --- /dev/null +++ b/biology/fermi-lite/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1722640889 +SHA256 (lh3-fermi-lite-v0.1-13-g85f159e_GH0.tar.gz) = eafa2f290c3857bcae4804fa3e86c59b8437777835cc601699d78e2192ca44fd +SIZE (lh3-fermi-lite-v0.1-13-g85f159e_GH0.tar.gz) = 248339 diff --git a/biology/fermi-lite/pkg-descr b/biology/fermi-lite/pkg-descr new file mode 100644 index 000000000000..f020c272f73e --- /dev/null +++ b/biology/fermi-lite/pkg-descr @@ -0,0 +1,8 @@ +Fermi-lite is a standalone C library as well as a command-line tool for +assembling Illumina short reads in regions from 100bp to 10 million bp in size. +It is largely a light-weight in-memory version of fermikit without generating +any intermediate files. It inherits the performance, the relatively small memory +footprint and the features of fermikit. In particular, fermi-lite is able to +retain heterozygous events and thus can be used to assemble diploid regions for +the purpose of variant calling. It is one of the limited choices for local +re-assembly and arguably the easiest to interface.