Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 466378) +++ head/biology/Makefile (revision 466379) @@ -1,126 +1,127 @@ # $FreeBSD$ # 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 += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha SUBDIR += stacks SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/seqtk/Makefile =================================================================== --- head/biology/seqtk/Makefile (nonexistent) +++ head/biology/seqtk/Makefile (revision 466379) @@ -0,0 +1,21 @@ +# $FreeBSD$ + +PORTNAME= seqtk +DISTVERSION= 1.2-8 +DISTVERSIONSUFFIX= -gd210c57 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Tool for processing sequences in FASTA/FASTQ format + +LICENSE= GPLv2 + +USE_GITHUB= yes +GH_ACCOUNT= lh3 + +PLIST_FILES= bin/seqtk + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/seqtk ${STAGEDIR}${PREFIX}/bin + +.include Property changes on: head/biology/seqtk/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/seqtk/distinfo =================================================================== --- head/biology/seqtk/distinfo (nonexistent) +++ head/biology/seqtk/distinfo (revision 466379) @@ -0,0 +1,3 @@ +TIMESTAMP = 1522780777 +SHA256 (lh3-seqtk-1.2-8-gd210c57_GH0.tar.gz) = 557317aab7f8cc306a98cd1148449f1e2edd7cd7c78ad5254ba955dfee518fa0 +SIZE (lh3-seqtk-1.2-8-gd210c57_GH0.tar.gz) = 21166 Property changes on: head/biology/seqtk/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/seqtk/files/patch-Makefile =================================================================== --- head/biology/seqtk/files/patch-Makefile (nonexistent) +++ head/biology/seqtk/files/patch-Makefile (revision 466379) @@ -0,0 +1,20 @@ +--- Makefile.orig 2017-11-07 19:42:14 UTC ++++ Makefile +@@ -1,10 +1,11 @@ +-CC=gcc +-CFLAGS=-g -Wall -O2 -Wno-unused-function ++CC ?= gcc ++CFLAGS ?= -g -Wall -O2 -Wno-unused-function ++LDFLAGS += -lz -lm + +-all:seqtk ++all: seqtk + +-seqtk:seqtk.c khash.h kseq.h +- $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm ++seqtk: seqtk.c khash.h kseq.h ++ $(CC) $(CFLAGS) seqtk.c -o $@ $(LDFLAGS) + + clean: +- rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session* ++ rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session* Property changes on: head/biology/seqtk/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/seqtk/pkg-descr =================================================================== --- head/biology/seqtk/pkg-descr (nonexistent) +++ head/biology/seqtk/pkg-descr (revision 466379) @@ -0,0 +1,6 @@ +Seqtk is a fast and lightweight tool for processing sequences in the FASTA or +FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be +optionally compressed by gzip. It performs basic file conversions and edits +much like standard Unix tools do with text files. + +WWW: https://github.com/lh3/seqtk Property changes on: head/biology/seqtk/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