Import scythe-2016.02.10 as wip/scythe.

[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 10:30:56 2016 -0500
Changeset:	e8f7fcdec4f4744bb00edd172239a30ecd00b93b

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

Log Message:
Import scythe-2016.02.10 as wip/scythe.

Scythe uses a Naive Bayesian approach to classify
contaminant substrings in sequence reads. It considers
quality information, which can make it robust in picking
out 3'-end adapters, which often include poor quality bases.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e8f7fcdec4f4744bb00edd172239a30ecd00b93b

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

diffstat:
 scythe/DESCR                  |  4 +++
 scythe/Makefile               | 61 +++++++++++++++++++++++++++++++++++++++++++
 scythe/PLIST                  |  2 ++
 scythe/TODO                   |  1 +
 scythe/distinfo               |  7 +++++
 scythe/patches/patch-Makefile | 13 +++++++++
 6 files changed, 88 insertions(+)

diffs:
diff --git a/scythe/DESCR b/scythe/DESCR
new file mode 100644
index 0000000..7046e0e
--- /dev/null
+++ b/scythe/DESCR
@@ -0,0 +1,4 @@
+Scythe uses a Naive Bayesian approach to classify
+contaminant substrings in sequence reads. It considers
+quality information, which can make it robust in picking
+out 3'-end adapters, which often include poor quality bases.
diff --git a/scythe/Makefile b/scythe/Makefile
new file mode 100644
index 0000000..49b6067
--- /dev/null
+++ b/scythe/Makefile
@@ -0,0 +1,61 @@
+# $NetBSD$
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+## Created by: Dan Siercks
+## $FreeBSD$
+#PLIST_FILES=	bin/scythe
+#do-install:
+#	${INSTALL_PROGRAM} ${WRKSRC}/scythe \
+#		${DESTDIR}${PREFIX}/bin
+#.include <bsd.port.mk>
+
+DISTNAME=	scythe-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=vsbuffalo/}
+GITHUB_PROJECT=	scythe
+GITHUB_TAG=	20d3cff7d7f483bd779aff75f861e93708c0a2b5
+
+MAINTAINER=	dsiercks%uwm.edu@localhost
+HOMEPAGE=	https://github.com/vsbuffalo/scythe
+COMMENT=	3'-end adapter contaminant trimmer
+# 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
+
+WRKSRC=		${WRKDIR}/scythe-${GITHUB_TAG}
+
+FETCH_USING=	curl
+
+PORTVERSION=	2016.02.10
+#DATADIR=	${PREFIX}/share/scythe
+#DOCSDIR=	${PREFIX}/share/doc/scythe
+
+# 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}/scythe ${DESTDIR}${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/scythe/PLIST b/scythe/PLIST
new file mode 100644
index 0000000..1d6d194
--- /dev/null
+++ b/scythe/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/scythe
diff --git a/scythe/TODO b/scythe/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/scythe/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/scythe/distinfo b/scythe/distinfo
new file mode 100644
index 0000000..af02f17
--- /dev/null
+++ b/scythe/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (scythe-2016.02.10-20d3cff7d7f483bd779aff75f861e93708c0a2b5.tar.gz) = 1076fe06c1cf4c9f82c115d31f1f1a4265448d85
+RMD160 (scythe-2016.02.10-20d3cff7d7f483bd779aff75f861e93708c0a2b5.tar.gz) = 50c276a86951e8370906936c6e78ac326812eb6c
+SHA512 (scythe-2016.02.10-20d3cff7d7f483bd779aff75f861e93708c0a2b5.tar.gz) = 437510971d7550dafd25521c5af87c7e1285fce42b966d38623ca98cd94aa41654dc84fbb93f5c3117001c7ddea5bb0da82bf6e7815a414703fd7e3f4cc0a2eb
+Size (scythe-2016.02.10-20d3cff7d7f483bd779aff75f861e93708c0a2b5.tar.gz) = 463781 bytes
+SHA1 (patch-Makefile) = 8b006650478acdcc8728e87261d655681ff4585b
diff --git a/scythe/patches/patch-Makefile b/scythe/patches/patch-Makefile
new file mode 100644
index 0000000..ca67ec2
--- /dev/null
+++ b/scythe/patches/patch-Makefile
@@ -0,0 +1,13 @@
+$NetBSD$
+
+# Allowing CC override
+--- Makefile.orig	2016-04-08 13:09:23.860500120 +0000
++++ Makefile
+@@ -1,6 +1,6 @@
+ PROGRAM_NAME = scythe
+ VERSION = 0.991
+-CC = gcc
++CC ?= gcc
+ DEBUG ?= 0
+ CFLAGS = -Wall -pedantic -DVERSION=$(VERSION) -std=gnu99
+ ifeq ($(DEBUG), 1)