Date: Tue, 3 Apr 2018 18:23:54 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r466367 - in head/biology: . trimadap trimadap/files Message-ID: <201804031823.w33INsKh068020@repo.freebsd.org>
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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@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
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