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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 <bsd.port.mk>
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 <pthread.h>
+ #include <stdlib.h>
+ #include <limits.h>
++#include <inttypes.h>
+
+ /************
+ * 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

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