Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 466234) +++ head/biology/Makefile (revision 466235) @@ -1,124 +1,125 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib 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 += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene 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 += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-macs2 SUBDIR += py-pysam 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 += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha SUBDIR += stacks SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/rainbow/Makefile =================================================================== --- head/biology/rainbow/Makefile (nonexistent) +++ head/biology/rainbow/Makefile (revision 466235) @@ -0,0 +1,26 @@ +# $FreeBSD$ + +PORTNAME= rainbow +DISTVERSION= 2.0.4 +CATEGORIES= biology +MASTER_SITES= SF/bio-rainbow +DISTNAME= rainbow_${PORTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Efficient clustering and assembling of short reads, especially for RAD + +LICENSE= GPLv3+ + +USES= gmake + +PLIST_FILES= bin/rainbow bin/ezmsim bin/rbasm + +do-install: + @${MKDIR} ${STAGEDIR}${PREFIX}/bin + ${INSTALL_PROGRAM} \ + ${WRKSRC}/rainbow \ + ${WRKSRC}/ezmsim \ + ${WRKSRC}/rbasm \ + ${STAGEDIR}${PREFIX}/bin + +.include Property changes on: head/biology/rainbow/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/rainbow/distinfo =================================================================== --- head/biology/rainbow/distinfo (nonexistent) +++ head/biology/rainbow/distinfo (revision 466235) @@ -0,0 +1,3 @@ +TIMESTAMP = 1520455667 +SHA256 (rainbow_2.0.4.tar.gz) = 79281aae3bccd1ad467afef6fc7c8327aaa8d56f538821e2833d2b8f26b5bafc +SIZE (rainbow_2.0.4.tar.gz) = 77111 Property changes on: head/biology/rainbow/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ 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/rainbow/files/patch-Makefile =================================================================== --- head/biology/rainbow/files/patch-Makefile (nonexistent) +++ head/biology/rainbow/files/patch-Makefile (revision 466235) @@ -0,0 +1,10 @@ +--- Makefile.orig 2015-07-27 18:28:54 UTC ++++ Makefile +@@ -1,5 +1,5 @@ +-CC=gcc +-CFLAGS= -W -O2 -Wall -Wno-self-assign -Wno-unused-function ++CC?=gcc ++CFLAGS?= -W -O2 -Wall -Wno-self-assign -Wno-unused-function + DFLAGS= -D_FILE_OFFSET_BITS=64 + GLIBS=-lm + GENERIC_SRC= string.h bitvec.h file_reader.h hashset.h sort.h list.h dna.h heap.h stdaln.h vector.h Property changes on: head/biology/rainbow/files/patch-Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ 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/rainbow/pkg-descr =================================================================== --- head/biology/rainbow/pkg-descr (nonexistent) +++ head/biology/rainbow/pkg-descr (revision 466235) @@ -0,0 +1,10 @@ +Rainbow provides an ultra-fast and memory-efficient solution to clustering and +assembling short genetic sequence reads produced by Restriction site Associated +DNA Sequencing (RAD-seq). It does this by, first, clustering reads using a +spaced seed method, then it divides potential groups into haplotypes in a +top-down manner. Next, along a guide tree, it iteratively merges sibling +leaves in a bottom-up manner if they are similar enough. Finally, Rainbow uses +a greedy algorithm to locally assemble merged reads into contigs. Both optimal +and suboptimal assembly results are output. + +WWW: http://sourceforge.net/projects/bio-rainbow/ Property changes on: head/biology/rainbow/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ 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