seqtk: Update to 1.4, imported from FreeBSD ports

[Jason W. Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Tue May 23 17:48:51 2023 -0500
Changeset:	ced2d7fbb01cfdb8fc1052aa54df31d9593c08cc

Modified Files:
	seqtk/DESCR
	seqtk/Makefile
	seqtk/distinfo
	seqtk/patches/patch-Makefile
Removed Files:
	seqtk/TODO

Log Message:
seqtk: Update to 1.4, imported from FreeBSD ports

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=ced2d7fbb01cfdb8fc1052aa54df31d9593c08cc

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 seqtk/DESCR                  |  7 ++++---
 seqtk/Makefile               | 13 +++----------
 seqtk/TODO                   |  1 -
 seqtk/distinfo               |  8 ++++----
 seqtk/patches/patch-Makefile | 37 +++++++++++++++++++++++++++----------
 5 files changed, 38 insertions(+), 28 deletions(-)

diffs:
diff --git a/seqtk/DESCR b/seqtk/DESCR
index ca4a4a1ece..d8d6aa596e 100644
--- a/seqtk/DESCR
+++ b/seqtk/DESCR
@@ -1,3 +1,4 @@
-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.
+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.
diff --git a/seqtk/Makefile b/seqtk/Makefile
index 97e2368334..739b3e7106 100644
--- a/seqtk/Makefile
+++ b/seqtk/Makefile
@@ -1,22 +1,15 @@
 # $NetBSD$
 
-DISTNAME=	seqtk-${PORTVERSION}
+DISTNAME=	seqtk-1.4
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=lh3/}
-GITHUB_PROJECT=	seqtk
-GITHUB_TAG=	d210c57d2ffa33da147e50f04f5aaaab1c160c8c
+GITHUB_TAG=	v${PKGVERSION_NOREV}
 
-MAINTAINER=	bacon%NetBSD.org@localhost
+OWNER=		bacon%NetBSD.org@localhost
 HOMEPAGE=	https://github.com/lh3/seqtk
 COMMENT=	Tool for processing sequences in FASTA/FASTQ format
 LICENSE=	gnu-gpl-v2
 
-PORTVERSION=	1.2.20171107
-
 INSTALLATION_DIRS=	bin
 
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/seqtk ${DESTDIR}${PREFIX}/bin
-
-.include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/seqtk/TODO b/seqtk/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/seqtk/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/seqtk/distinfo b/seqtk/distinfo
index 0b15fa2a42..7ed24cfdde 100644
--- a/seqtk/distinfo
+++ b/seqtk/distinfo
@@ -1,6 +1,6 @@
 $NetBSD$
 
-RMD160 (seqtk-1.2.20171107-d210c57d2ffa33da147e50f04f5aaaab1c160c8c.tar.gz) = e6c2698f2c0e9e4b2bdb2a91f1e6b849cb638020
-SHA512 (seqtk-1.2.20171107-d210c57d2ffa33da147e50f04f5aaaab1c160c8c.tar.gz) = 696aeba59726a78cec59bea9b31b80bb7d45bb15273330789990e0ff6d28c07147810ab5850820b2d176284b7d3eaceeb3bc4fb1475a180784df4ce76af000f4
-Size (seqtk-1.2.20171107-d210c57d2ffa33da147e50f04f5aaaab1c160c8c.tar.gz) = 21165 bytes
-SHA1 (patch-Makefile) = 89c7ee1cc8ba6315d9b83ae674c92bf9a58e2eee
+BLAKE2s (seqtk-1.4.tar.gz) = e5003661166ace64fdaf3856e23d13163ebe2d5aa3f7a684ff44f76abca5768b
+SHA512 (seqtk-1.4.tar.gz) = d94ff75e23c9c63c948fd5ba23b52ca29df709c2fef76ee201342b4f32c53cf79366b55f05a689071d1b35770e01344787a87ce590b86c542ddc7c4ae393c8a1
+Size (seqtk-1.4.tar.gz) = 23748 bytes
+SHA1 (patch-Makefile) = ca2f5027384d3803a99e7ef5fec3486afa336751
diff --git a/seqtk/patches/patch-Makefile b/seqtk/patches/patch-Makefile
index d069cf8e5e..8cef0d1ca8 100644
--- a/seqtk/patches/patch-Makefile
+++ b/seqtk/patches/patch-Makefile
@@ -1,20 +1,37 @@
 $NetBSD$
 
-# Respect env
-
---- Makefile.orig	2017-11-07 19:42:14.000000000 +0000
+--- Makefile.orig	2018-06-18 00:15:09 UTC
 +++ Makefile
-@@ -1,10 +1,10 @@
+@@ -1,14 +1,23 @@
 -CC=gcc
 -CFLAGS=-g -Wall -O2 -Wno-unused-function
-+CC	?= gcc
-+CFLAGS	?= -g -Wall -O2 -Wno-unused-function
+-BINDIR=/usr/local/bin
  
- all:seqtk
+-all:seqtk
++# Respect user's build environment by using ?= to set defaults for variables
++# not set in the env or make arguments.  Use += to add essential args.
  
- seqtk:seqtk.c khash.h kseq.h
+-seqtk:seqtk.c khash.h kseq.h
 -		$(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm
-+		$(CC) $(CFLAGS) seqtk.c -o $@ $(LDFLAGS) -lz -lm
++CC	?= gcc
++CFLAGS	?= -g -Wall -O2 -Wno-unused-function
++LDFLAGS	+= -lz -lm
++PREFIX	?= /usr/local
++MKDIR	?= mkdir
++INSTALL	?= install
++# DESTDIR is empty by default to install straight to PREFIX
+ 
+-install:all
+-		install seqtk $(BINDIR)
++all: seqtk
  
++seqtk: seqtk.c khash.h kseq.h
++	$(CC) $(CFLAGS) seqtk.c -o $@ $(LDFLAGS)
++
++install: all
++	$(MKDIR) -p $(DESTDIR)$(PREFIX)/bin
++	$(INSTALL) -c -m 0755 seqtk $(DESTDIR)$(PREFIX)/bin
++
  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*
++	rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*