trimadap: Tool for processing sequences in FASTA/FASTQ format

[root <root%centosdev.ceas.uwm.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	root <root%centosdev.ceas.uwm.edu@localhost>
Pushed By:	outpaddling
Date:		Thu Mar 22 16:48:23 2018 -0500
Changeset:	585f77de0dc2bb5a8a813b74479a258322f9275a

Added Files:
	trimadap/DESCR
	trimadap/Makefile
	trimadap/PLIST
	trimadap/distinfo
	trimadap/patches/patch-Makefile
	trimadap/patches/patch-kthread.c

Log Message:
trimadap: Tool for processing sequences in FASTA/FASTQ format

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=585f77de0dc2bb5a8a813b74479a258322f9275a

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

diffstat:
 trimadap/DESCR                   |  3 +++
 trimadap/Makefile                | 35 +++++++++++++++++++++++++++++++++++
 trimadap/PLIST                   |  2 ++
 trimadap/distinfo                |  8 ++++++++
 trimadap/patches/patch-Makefile  | 13 +++++++++++++
 trimadap/patches/patch-kthread.c | 13 +++++++++++++
 6 files changed, 74 insertions(+)

diffs:
diff --git a/trimadap/DESCR b/trimadap/DESCR
new file mode 100644
index 0000000000..ca4a4a1ece
--- /dev/null
+++ b/trimadap/DESCR
@@ -0,0 +1,3 @@
+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.
diff --git a/trimadap/Makefile b/trimadap/Makefile
new file mode 100644
index 0000000000..ecf52e2fda
--- /dev/null
+++ b/trimadap/Makefile
@@ -0,0 +1,35 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Tue Mar  6 13:47:17 CST 2018               #
+###########################################################
+
+DISTNAME=	trimadap-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=lh3/}
+GITHUB_PROJECT=	trimadap
+GITHUB_TAG=	ddfef210563830d9193b40949da3523b6fb93003
+
+MAINTAINER=	dsiercks%uwm.edu@localhost
+HOMEPAGE=	https://github.com/lh3/seqtk
+COMMENT=	Tool for processing sequences in FASTA/FASTQ format
+LICENSE=	gnu-gpl-v2
+
+WRKSRC=		${WRKDIR}/trimadap-${GITHUB_TAG}
+
+PORTVERSION=	0.1.20170211
+
+# FIXME: Come up with a better patch that can be sent upstream
+SUBST_CLASSES+=		libz
+SUBST_STAGE.libz=	post-patch
+SUBST_SED.libz+=	-e "s|-lz|-L${PREFIX}/lib -lz|g"
+SUBST_FILES.libz+=	${WRKSRC}/Makefile
+
+INSTALLATION_DIRS=	bin
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/trimadap-mt ${DESTDIR}${PREFIX}/bin
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/trimadap/PLIST b/trimadap/PLIST
new file mode 100644
index 0000000000..93b9ae973d
--- /dev/null
+++ b/trimadap/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/trimadap-mt
diff --git a/trimadap/distinfo b/trimadap/distinfo
new file mode 100644
index 0000000000..6028a58d02
--- /dev/null
+++ b/trimadap/distinfo
@@ -0,0 +1,8 @@
+$NetBSD$
+
+SHA1 (trimadap-0.1.20170211-ddfef210563830d9193b40949da3523b6fb93003.tar.gz) = 30705541cc8c68ea3bfeb5d2bdbc6fcf3e55e51d
+RMD160 (trimadap-0.1.20170211-ddfef210563830d9193b40949da3523b6fb93003.tar.gz) = 95019d0ed6aa478efa9126a6446afc71ea054f6d
+SHA512 (trimadap-0.1.20170211-ddfef210563830d9193b40949da3523b6fb93003.tar.gz) = 364683285fd5f52df33e637f2ca9756b00a24acb45ea3a9ccddaf4126ee30e3f4e1150f56b0e5404f62b010374000eb6768c16ef17954356ffba7d1f28c01c86
+Size (trimadap-0.1.20170211-ddfef210563830d9193b40949da3523b6fb93003.tar.gz) = 13133 bytes
+SHA1 (patch-Makefile) = 3c1208c10b83461280a53e6b14f9d2a73481947b
+SHA1 (patch-kthread.c) = 40cfaaf734b0eed0da13f698d2e31d55f189f272
diff --git a/trimadap/patches/patch-Makefile b/trimadap/patches/patch-Makefile
new file mode 100644
index 0000000000..b25fe4aea3
--- /dev/null
+++ b/trimadap/patches/patch-Makefile
@@ -0,0 +1,13 @@
+$NetBSD$
+
+#Use the correct compiler variable (CXX, not CC) and respect the environment
+--- Makefile.orig	2017-02-11 22:31:35 UTC
++++ Makefile
+@@ -1,5 +1,5 @@
+-CC=gcc
+-CFLAGS=-g -Wall -O2 -Wno-unused-function
++CC ?=		gcc
++CFLAGS ?=	-g -Wall -O2 -Wno-unused-function
+ 
+ all:trimadap-mt
+ 
diff --git a/trimadap/patches/patch-kthread.c b/trimadap/patches/patch-kthread.c
new file mode 100644
index 0000000000..4384b6438c
--- /dev/null
+++ b/trimadap/patches/patch-kthread.c
@@ -0,0 +1,13 @@
+$NetBSD$
+
+# include inttypes
+--- 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() *