svn commit: r466367 - in head/biology: . trimadap trimadap/files

[Jason W. Bacon]

Author: jwb
Date: Tue Apr  3 18:23:54 2018
New Revision: 466367
URL: https://svnweb.freebsd.org/changeset/ports/466367

Log:
  biology/trimadap: Trim adapter sequences from Illumina data
  
  Reviewed by:    mat
  Approved by:    jrm
  Differential Revision:  https://reviews.freebsd.org/D14935

Added:
  head/biology/trimadap/
  head/biology/trimadap/Makefile   (contents, props changed)
  head/biology/trimadap/distinfo   (contents, props changed)
  head/biology/trimadap/files/
  head/biology/trimadap/files/patch-Makefile   (contents, props changed)
  head/biology/trimadap/files/patch-kthread.c   (contents, props changed)
  head/biology/trimadap/pkg-descr   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Tue Apr  3 18:03:08 2018	(r466366)
+++ head/biology/Makefile	Tue Apr  3 18:23:54 2018	(r466367)
@@ -115,6 +115,7 @@
     SUBDIR += t_coffee
     SUBDIR += tinker
     SUBDIR += treepuzzle
+    SUBDIR += trimadap
     SUBDIR += trimmomatic
     SUBDIR += ugene
     SUBDIR += vcftools

Added: head/biology/trimadap/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/trimadap/Makefile	Tue Apr  3 18:23:54 2018	(r466367)
@@ -0,0 +1,23 @@
+# $FreeBSD$
+
+PORTNAME=	trimadap
+DISTVERSION=	0.1-3
+DISTVERSIONSUFFIX=	-gddfef21
+CATEGORIES=	biology
+
+MAINTAINER=	jwb at 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>

Added: head/biology/trimadap/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/trimadap/distinfo	Tue Apr  3 18:23:54 2018	(r466367)
@@ -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

Added: head/biology/trimadap/files/patch-Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/trimadap/files/patch-Makefile	Tue Apr  3 18:23:54 2018	(r466367)
@@ -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

Added: head/biology/trimadap/files/patch-kthread.c
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/trimadap/files/patch-kthread.c	Tue Apr  3 18:23:54 2018	(r466367)
@@ -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() *

Added: head/biology/trimadap/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/trimadap/pkg-descr	Tue Apr  3 18:23:54 2018	(r466367)
@@ -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