svn commit: r466379 - in head/biology: . seqtk seqtk/files

[Jason W. Bacon]

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 at 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