Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 466366) +++ head/biology/Makefile (revision 466367) @@ -1,125 +1,126 @@ # $FreeBSD$ # 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 += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/trimadap/Makefile =================================================================== --- head/biology/trimadap/Makefile (nonexistent) +++ head/biology/trimadap/Makefile (revision 466367) @@ -0,0 +1,23 @@ +# $FreeBSD$ + +PORTNAME= trimadap +DISTVERSION= 0.1-3 +DISTVERSIONSUFFIX= -gddfef21 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Trim adapter sequences from Illumina data using heuristic rules + +LICENSE= GPLv2 + +USE_GITHUB= yes +GH_ACCOUNT= lh3 + +PLIST_FILES= bin/trimadap-mt + +CFLAGS_i386= -msse2 + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/trimadap-mt ${STAGEDIR}${PREFIX}/bin + +.include Property changes on: head/biology/trimadap/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/trimadap/distinfo =================================================================== --- head/biology/trimadap/distinfo (nonexistent) +++ head/biology/trimadap/distinfo (revision 466367) @@ -0,0 +1,3 @@ +TIMESTAMP = 1522773176 +SHA256 (lh3-trimadap-0.1-3-gddfef21_GH0.tar.gz) = c2c42a3257d37b12be3523ed0d4415bddd401d72b99b05ba4ae33afaa3c3f373 +SIZE (lh3-trimadap-0.1-3-gddfef21_GH0.tar.gz) = 13138 Property changes on: head/biology/trimadap/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/trimadap/files/patch-Makefile =================================================================== --- head/biology/trimadap/files/patch-Makefile (nonexistent) +++ head/biology/trimadap/files/patch-Makefile (revision 466367) @@ -0,0 +1,20 @@ +--- Makefile.orig 2017-02-11 22:31:35 UTC ++++ Makefile +@@ -1,10 +1,12 @@ +-CC=gcc +-CFLAGS=-g -Wall -O2 -Wno-unused-function ++CC ?= gcc ++CFLAGS ?= -g -Wall -O2 -Wno-unused-function ++LDFLAGS += -lz -lm + +-all:trimadap-mt ++all: trimadap-mt + + trimadap-mt:trimadap-mt.c ksw.c kthread.c kseq.h ksw.h +- $(CC) $(CFLAGS) -pthread ksw.c kthread.c trimadap-mt.c -o $@ -lz -lm ++ $(CC) $(CFLAGS) -pthread ksw.c kthread.c trimadap-mt.c -o $@ $(LDFLAGS) + + clean: +- rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session* trimadap-mt ++ rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a \ ++ *.dSYM session* trimadap-mt Property changes on: head/biology/trimadap/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/trimadap/files/patch-kthread.c =================================================================== --- head/biology/trimadap/files/patch-kthread.c (nonexistent) +++ head/biology/trimadap/files/patch-kthread.c (revision 466367) @@ -0,0 +1,10 @@ +--- kthread.c.orig 2017-02-11 22:31:35 UTC ++++ kthread.c +@@ -1,6 +1,7 @@ + #include + #include + #include ++#include + + /************ + * kt_for() * Property changes on: head/biology/trimadap/files/patch-kthread.c ___________________________________________________________________ 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/trimadap/pkg-descr =================================================================== --- head/biology/trimadap/pkg-descr (nonexistent) +++ head/biology/trimadap/pkg-descr (revision 466367) @@ -0,0 +1,8 @@ +Trimadap is a small tool to trim adapter sequences from Illumina data. It +performs SSE2-SW between each read and each adapter sequence and identifies +adapter sequences with a few heuristic rules which can be found in the +ta_trim1() function in trimadap-mt.c. The default adapters it uses are included +in illumina.txt. These are typical Illumina adapters from paired-end +sequencing. + +WWW: https://github.com/lh3/trimadap Property changes on: head/biology/trimadap/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