Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 499894) +++ head/biology/Makefile (revision 499895) @@ -1,161 +1,162 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += consed SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate + SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate 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-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-xenaPython SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise .include Index: head/biology/minimap2/Makefile =================================================================== --- head/biology/minimap2/Makefile (nonexistent) +++ head/biology/minimap2/Makefile (revision 499895) @@ -0,0 +1,25 @@ +# $FreeBSD$ + +PORTNAME= minimap2 +DISTVERSIONPREFIX= v +DISTVERSION= 2.16 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Pairwise aligner for genomic and spliced nucleotide sequences + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +# Depends on hard-coded SSE instructions +# There appears to be some support for AARCH64 as well +ONLY_FOR_ARCHS= amd64 i386 + +USES= gmake +USE_GITHUB= yes +GH_ACCOUNT= lh3 + +INSTALL_TARGET= install-strip +PLIST_FILES= bin/minimap2 man/man1/minimap2.1.gz + +.include Property changes on: head/biology/minimap2/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/minimap2/distinfo =================================================================== --- head/biology/minimap2/distinfo (nonexistent) +++ head/biology/minimap2/distinfo (revision 499895) @@ -0,0 +1,3 @@ +TIMESTAMP = 1555901297 +SHA256 (lh3-minimap2-v2.16_GH0.tar.gz) = 9d4f1c9f1c2b29c2560b7ad53b2210dabd82161a0f88184f423534bd289433c3 +SIZE (lh3-minimap2-v2.16_GH0.tar.gz) = 221287 Property changes on: head/biology/minimap2/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/minimap2/files/patch-Makefile =================================================================== --- head/biology/minimap2/files/patch-Makefile (nonexistent) +++ head/biology/minimap2/files/patch-Makefile (revision 499895) @@ -0,0 +1,40 @@ +--- Makefile.orig 2019-02-28 20:49:24 UTC ++++ Makefile +@@ -1,11 +1,19 @@ +-CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra +-CPPFLAGS= -DHAVE_KALLOC ++CFLAGS?= -g -Wall -O2 ++CFLAGS+= -Wc++-compat #-Wextra ++CPPFLAGS+= -DHAVE_KALLOC + INCLUDES= + OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o + PROG= minimap2 + PROG_EXTRA= sdust minimap2-lite + LIBS= -lm -lz -lpthread + ++PREFIX?= /usr/local ++DESTDIR?= . ++MAN1DIR?= ${PREFIX}/man/man1 ++MKDIR?= mkdir ++INSTALL?= install ++STRIP?= strip ++ + ifeq ($(arm_neon),) # if arm_neon is not defined + ifeq ($(sse2only),) # if sse2only is not defined + OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o +@@ -84,6 +92,15 @@ ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h + $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@ + + # other non-file targets ++ ++install: all ++ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin ++ ${MKDIR} -p ${DESTDIR}${MAN1DIR} ++ ${INSTALL} -c minimap2 ${DESTDIR}${PREFIX}/bin ++ ${INSTALL} -c minimap2.1 ${DESTDIR}${MAN1DIR} ++ ++install-strip: install ++ ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2 + + clean: + rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg* Property changes on: head/biology/minimap2/files/patch-Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/minimap2/pkg-descr =================================================================== --- head/biology/minimap2/pkg-descr (nonexistent) +++ head/biology/minimap2/pkg-descr (revision 499895) @@ -0,0 +1,18 @@ +Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA +sequences against a large reference database. Typical use cases include: + +(1) mapping PacBio or Oxford Nanopore genomic reads to the human genome + +(2) finding overlaps between long reads with error rate up to ~15% + +(3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA + readsagainst a reference genome + +(4) aligning Illumina single- or paired-end reads + +(5) assembly-to-assembly alignment + +(6) full-genome alignment between two closely related species with divergence + below ~15% + +WWW: https://github.com/lh3/minimap2 Property changes on: head/biology/minimap2/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property