Import sickle-1.33 as wip/sickle.

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 10:32:18 2016 -0500
Changeset:	a9ef69ed16c3796a1d2825d1ee1ab30a1514e9d3

Added Files:
	sickle/DESCR
	sickle/Makefile
	sickle/PLIST
	sickle/TODO
	sickle/distinfo
	sickle/patches/patch-Makefile

Log Message:
Import sickle-1.33 as wip/sickle.

Sickle is a tool that uses sliding windows along with
quality and length thresholds to determine when quality
is sufficiently low to trim the 3'-end of reads and
also determines when the quality is sufficiently high
enough to trim the 5'-end of reads.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a9ef69ed16c3796a1d2825d1ee1ab30a1514e9d3

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

diffstat:
 sickle/DESCR                  |  5 ++++
 sickle/Makefile               | 63 +++++++++++++++++++++++++++++++++++++++++++
 sickle/PLIST                  |  2 ++
 sickle/TODO                   |  1 +
 sickle/distinfo               |  7 +++++
 sickle/patches/patch-Makefile | 31 +++++++++++++++++++++
 6 files changed, 109 insertions(+)

diffs:
diff --git a/sickle/DESCR b/sickle/DESCR
new file mode 100644
index 0000000..bfa67eb
--- /dev/null
+++ b/sickle/DESCR
@@ -0,0 +1,5 @@
+Sickle is a tool that uses sliding windows along with
+quality and length thresholds to determine when quality
+is sufficiently low to trim the 3'-end of reads and
+also determines when the quality is sufficiently high
+enough to trim the 5'-end of reads.
diff --git a/sickle/Makefile b/sickle/Makefile
new file mode 100644
index 0000000..c7780f9
--- /dev/null
+++ b/sickle/Makefile
@@ -0,0 +1,63 @@
+# $NetBSD$
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+## Created by: Dan Siercks
+## $FreeBSD$
+#DISTVERSIONPREFIX=      v
+## Requires libz
+#PLIST_FILES=	bin/sickle
+#do-install:
+#	${INSTALL_PROGRAM} ${WRKSRC}/sickle \
+#		${DESTDIR}${PREFIX}/bin
+#.include <bsd.port.mk>
+
+DISTNAME=	sickle-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=najoshi/}
+GITHUB_PROJECT=	sickle
+GITHUB_TAG=	v${PORTVERSION}
+
+MAINTAINER=	dsiercks%uwm.edu@localhost
+HOMEPAGE=	https://github.com/najoshi/sickle
+COMMENT=	Windowed adaptive trimming tool for FASTQ files using quality
+# Check this
+LICENSE=	gnu-gpl-v2
+
+# Test and change if necessary.
+# MAKE_JOBS_SAFE=	no
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+
+FETCH_USING=	curl
+
+PORTVERSION=	1.33
+#DATADIR=	${PREFIX}/share/sickle
+#DOCSDIR=	${PREFIX}/share/doc/sickle
+
+# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
+# .include "../../mk/bsd.prefs.mk"
+
+# Keep this if there are user-selectable options.
+# .include "options.mk"
+
+# Specify which directories to create before install.
+# You should only need this if using your own install target.
+
+INSTALLATION_DIRS=	bin
+AUTO_MKDIRS=	yes
+do-install:
+#	${MKDIR} ${DESTDIR}${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/sickle ${DESTDIR}${PREFIX}/bin
+
+
+# Linux doesn't have zlib in the base, so just in case...
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/sickle/PLIST b/sickle/PLIST
new file mode 100644
index 0000000..0db9a91
--- /dev/null
+++ b/sickle/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/sickle
diff --git a/sickle/TODO b/sickle/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/sickle/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/sickle/distinfo b/sickle/distinfo
new file mode 100644
index 0000000..6089873
--- /dev/null
+++ b/sickle/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (sickle-1.33.tar.gz) = 593274fb7e12a52c9086dff69623aedca1799a5c
+RMD160 (sickle-1.33.tar.gz) = ca7e39beedb5330437947589083ee5fe9a63a42c
+SHA512 (sickle-1.33.tar.gz) = 94d9794861655c9d8688a4c71757ba93166f167ae529c5661998d287b93c6ccc9755d9e3db8d481bbd5dca4cf047f6266880a5fc1f8099e597bc857954404dcb
+Size (sickle-1.33.tar.gz) = 631275 bytes
+SHA1 (patch-Makefile) = 784469af2d5e1c0daf3633860b344c4d67ecf52e
diff --git a/sickle/patches/patch-Makefile b/sickle/patches/patch-Makefile
new file mode 100644
index 0000000..ab1460c
--- /dev/null
+++ b/sickle/patches/patch-Makefile
@@ -0,0 +1,31 @@
+$NetBSD$
+
+# patching Makefile
+--- Makefile.orig	2014-07-23 02:03:28 UTC
++++ Makefile
+@@ -1,16 +1,18 @@
+ PROGRAM_NAME = sickle
+ VERSION = 1.33
+-CC = gcc
+-CFLAGS = -Wall -pedantic -DVERSION=$(VERSION)
+-DEBUG = -g
+-OPT = -O3
++CC ?= gcc
++CFLAGS ?= -Wall -pedantic -DVERSION=$(VERSION)
++DEBUG ?= -g
++OPT ?= -O3
+ ARCHIVE = $(PROGRAM_NAME)_$(VERSION)
+-LDFLAGS=
+-LIBS = -lz
+-SDIR = src
++LDFLAGS ?=
++LIBS= -lz
++SDIR ?= src
+ 
+ .PHONY: clean default build distclean dist debug
+ 
++all:	build
++
+ default: build
+ 
+ sliding.o: $(SDIR)/sliding.c $(SDIR)/kseq.h $(SDIR)/sickle.h