Index: head/biology/Makefile =================================================================== --- head/biology/Makefile +++ head/biology/Makefile @@ -115,6 +115,7 @@ SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle + SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools Index: head/biology/trimadap/Makefile =================================================================== --- head/biology/trimadap/Makefile +++ head/biology/trimadap/Makefile @@ -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 Index: head/biology/trimadap/distinfo =================================================================== --- head/biology/trimadap/distinfo +++ head/biology/trimadap/distinfo @@ -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 Index: head/biology/trimadap/files/patch-Makefile =================================================================== --- head/biology/trimadap/files/patch-Makefile +++ head/biology/trimadap/files/patch-Makefile @@ -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 Index: head/biology/trimadap/files/patch-kthread.c =================================================================== --- head/biology/trimadap/files/patch-kthread.c +++ head/biology/trimadap/files/patch-kthread.c @@ -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() * Index: head/biology/trimadap/pkg-descr =================================================================== --- head/biology/trimadap/pkg-descr +++ head/biology/trimadap/pkg-descr @@ -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