Date: Tue, 3 Apr 2018 20:57:05 +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: r466379 - in head/biology: . seqtk seqtk/files Message-ID: <201804032057.w33Kv5ME098520@repo.freebsd.org>
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Author: jwb Date: Tue Apr 3 20:57:05 2018 New Revision: 466379 URL: https://svnweb.freebsd.org/changeset/ports/466379 Log: biology/seqtk: Tool for processing sequences in FASTA/FASTQ format Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14954 Added: head/biology/seqtk/ head/biology/seqtk/Makefile (contents, props changed) head/biology/seqtk/distinfo (contents, props changed) head/biology/seqtk/files/ head/biology/seqtk/files/patch-Makefile (contents, props changed) head/biology/seqtk/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Tue Apr 3 20:48:47 2018 (r466378) +++ head/biology/Makefile Tue Apr 3 20:57:05 2018 (r466379) @@ -106,6 +106,7 @@ SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio + SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust Added: head/biology/seqtk/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/seqtk/Makefile Tue Apr 3 20:57:05 2018 (r466379) @@ -0,0 +1,21 @@ +# $FreeBSD$ + +PORTNAME= seqtk +DISTVERSION= 1.2-8 +DISTVERSIONSUFFIX= -gd210c57 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Tool for processing sequences in FASTA/FASTQ format + +LICENSE= GPLv2 + +USE_GITHUB= yes +GH_ACCOUNT= lh3 + +PLIST_FILES= bin/seqtk + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/seqtk ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> Added: head/biology/seqtk/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/seqtk/distinfo Tue Apr 3 20:57:05 2018 (r466379) @@ -0,0 +1,3 @@ +TIMESTAMP = 1522780777 +SHA256 (lh3-seqtk-1.2-8-gd210c57_GH0.tar.gz) = 557317aab7f8cc306a98cd1148449f1e2edd7cd7c78ad5254ba955dfee518fa0 +SIZE (lh3-seqtk-1.2-8-gd210c57_GH0.tar.gz) = 21166 Added: head/biology/seqtk/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/seqtk/files/patch-Makefile Tue Apr 3 20:57:05 2018 (r466379) @@ -0,0 +1,20 @@ +--- Makefile.orig 2017-11-07 19:42:14 UTC ++++ Makefile +@@ -1,10 +1,11 @@ +-CC=gcc +-CFLAGS=-g -Wall -O2 -Wno-unused-function ++CC ?= gcc ++CFLAGS ?= -g -Wall -O2 -Wno-unused-function ++LDFLAGS += -lz -lm + +-all:seqtk ++all: seqtk + +-seqtk:seqtk.c khash.h kseq.h +- $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm ++seqtk: seqtk.c khash.h kseq.h ++ $(CC) $(CFLAGS) seqtk.c -o $@ $(LDFLAGS) + + clean: +- rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session* ++ rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session* Added: head/biology/seqtk/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/seqtk/pkg-descr Tue Apr 3 20:57:05 2018 (r466379) @@ -0,0 +1,6 @@ +Seqtk is a fast and lightweight tool for processing sequences in the FASTA or +FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be +optionally compressed by gzip. It performs basic file conversions and edits +much like standard Unix tools do with text files. + +WWW: https://github.com/lh3/seqtk
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