diff --git a/biology/Makefile b/biology/Makefile index 24a2bc0890c3..b3a5731f8a6a 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,212 +1,213 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools + SUBDIR += bfc SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc 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 += 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 += 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-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-goatools SUBDIR += py-gtfparse SUBDIR += py-hits 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-pyfaidx SUBDIR += py-pysam SUBDIR += py-python-libsbml 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 += 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/bfc/Makefile b/biology/bfc/Makefile new file mode 100644 index 000000000000..967e8829f16a --- /dev/null +++ b/biology/bfc/Makefile @@ -0,0 +1,20 @@ +PORTNAME= bfc +DISTVERSION= g20150417 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Correct sequencing errors from Illumina sequencing data + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +USES= gmake +USE_GITHUB= yes + +GH_ACCOUNT= lh3 +GH_TAGNAME= 69ab176e + +INSTALL_TARGET= install-strip +PLIST_FILES= bin/bfc bin/hash2cnt + +.include diff --git a/biology/bfc/distinfo b/biology/bfc/distinfo new file mode 100644 index 000000000000..b2e518d4e0c8 --- /dev/null +++ b/biology/bfc/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1629673065 +SHA256 (lh3-bfc-g20150417-69ab176e_GH0.tar.gz) = 202913e590421d23571c5e7c5cb9c23730ee57cb5b2eaa0e7806d33c49482452 +SIZE (lh3-bfc-g20150417-69ab176e_GH0.tar.gz) = 68138 diff --git a/biology/bfc/files/patch-Makefile b/biology/bfc/files/patch-Makefile new file mode 100644 index 000000000000..b031139aa596 --- /dev/null +++ b/biology/bfc/files/patch-Makefile @@ -0,0 +1,36 @@ +--- Makefile.orig 2015-04-17 05:17:58 UTC ++++ Makefile +@@ -1,11 +1,17 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once ++CC?= gcc ++# Allow env to set optimization and warning levels, then add required flags ++CFLAGS?= -g -Wall -O2 ++CFLAGS+= -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once + CPPFLAGS= + INCLUDES= + OBJS= kthread.o utils.o bseq.o bbf.o htab.o count.o correct.o bfc.o + PROG= bfc hash2cnt + LIBS= -lm -lz -lpthread + ++MKDIR?= mkdir ++INSTALL?= install ++STRIP?= strip ++ + .SUFFIXES:.c .o + + .c.o: +@@ -18,6 +24,13 @@ bfc:$(OBJS) + + hash2cnt:hash2cnt.o + $(CC) $(CFLAGS) $< -o $@ ++ ++install: ++ $(MKDIR) -p $(DESTDIR)$(PREFIX)/bin ++ $(INSTALL) -c $(PROG) $(DESTDIR)$(PREFIX)/bin ++ ++install-strip: install ++ $(STRIP) $(DESTDIR)$(PREFIX)/bin/* + + clean: + rm -fr gmon.out *.o ext/*.o a.out $(PROG) *~ *.a *.dSYM session* diff --git a/biology/bfc/files/patch-kthread.c b/biology/bfc/files/patch-kthread.c new file mode 100644 index 000000000000..a019b17beea5 --- /dev/null +++ b/biology/bfc/files/patch-kthread.c @@ -0,0 +1,10 @@ +--- kthread.c.orig 2021-08-22 22:59:48 UTC ++++ kthread.c +@@ -1,6 +1,7 @@ + #include + #include + #include ++#include + + /************ + * kt_for() * diff --git a/biology/bfc/pkg-descr b/biology/bfc/pkg-descr new file mode 100644 index 000000000000..a2135b6a4ecc --- /dev/null +++ b/biology/bfc/pkg-descr @@ -0,0 +1,6 @@ +BFC is a standalone high-performance tool for correcting sequencing +errors from Illumina sequencing data. It is specifically designed for +high-coverage whole-genome human data, though also performs well for +small genomes. + +WWW: https://github.com/lh3/bfc