Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/ bedtools2 bedtools2-2.23.0 as wip/bedtools2.

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/ bedtools2 bedtools2-2.23.0 as wip/bedtools2.
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Wed, 11 May 2016 19:07:39 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 14:07:39 2016 -0500
Changeset:	d3a5d0ac3df3dc65a1936610a93414aa18ebeec8

Added Files:
	bedtools2/DESCR
	bedtools2/Makefile
	bedtools2/PLIST
	bedtools2/TODO
	bedtools2/distinfo
	bedtools2/patches/patch-Makefile

Log Message:
Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/bedtools2
bedtools2-2.23.0 as wip/bedtools2.

Collectively, the bedtools utilities are a swiss-army knife of tools
for a wide-range of genomics analysis tasks. The most widely-used
tools enable genome arithmetic: that is, set theory on the genome.
For example, bedtools allows one to intersect, merge, count,
complement, and shuffle genomic intervals from multiple files in
widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
HTTP: https://github.com/arq5x/bedtools2

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d3a5d0ac3df3dc65a1936610a93414aa18ebeec8

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

diffstat:
 bedtools2/DESCR                  |  7 +++++
 bedtools2/Makefile               | 40 ++++++++++++++++++++++++
 bedtools2/PLIST                  | 38 +++++++++++++++++++++++
 bedtools2/TODO                   |  1 +
 bedtools2/distinfo               |  7 +++++
 bedtools2/patches/patch-Makefile | 66 ++++++++++++++++++++++++++++++++++++++++
 6 files changed, 159 insertions(+)

diffs:
diff --git a/bedtools2/DESCR b/bedtools2/DESCR
new file mode 100644
index 0000000..06e8189
--- /dev/null
+++ b/bedtools2/DESCR
@@ -0,0 +1,7 @@
+Collectively, the bedtools utilities are a swiss-army knife of tools 
+for a wide-range of genomics analysis tasks. The most widely-used 
+tools enable genome arithmetic: that is, set theory on the genome. 
+For example, bedtools allows one to intersect, merge, count, 
+complement, and shuffle genomic intervals from multiple files in 
+widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
+HTTP: https://github.com/arq5x/bedtools2
diff --git a/bedtools2/Makefile b/bedtools2/Makefile
new file mode 100644
index 0000000..4bb2d5a
--- /dev/null
+++ b/bedtools2/Makefile
@@ -0,0 +1,40 @@
+# $NetBSD$
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+# .if ${ARCH} == i386
+# MAKE_ENV+=	POPCNT_CAPABILITY=0
+# .endif
+# #INSTALL_TARGET=	install-strip
+# post-install:
+# 	${STRIP_CMD} ${DESTDIR}${PREFIX}/bin/bedtools
+
+DISTNAME=	bedtools2-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=arq5x/}
+GITHUB_TAG=	v${PORTVERSION}
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	
+COMMENT=	Swiss army knife for genome arithmetic
+LICENSE=	gnu-gpl-v2
+
+USE_LANGUAGES=	c c++ python
+USE_TOOLS+=	gmake
+
+WRKSRC=		${WRKDIR}/bedtools2-${PORTVERSION}
+
+MAKE_ENV=	PYTHONBIN=${PYTHONBIN}
+
+FETCH_USING=	curl
+
+PORTVERSION=	2.23.0
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/bedtools2/PLIST b/bedtools2/PLIST
new file mode 100644
index 0000000..78eafde
--- /dev/null
+++ b/bedtools2/PLIST
@@ -0,0 +1,38 @@
+@comment $NetBSD$
+bin/annotateBed
+bin/bamToBed
+bin/bamToFastq
+bin/bed12ToBed6
+bin/bedpeToBam
+bin/bedToBam
+bin/bedToIgv
+bin/bedtools
+bin/closestBed
+bin/clusterBed
+bin/complementBed
+bin/coverageBed
+bin/expandCols
+bin/fastaFromBed
+bin/flankBed
+bin/genomeCoverageBed
+bin/getOverlap
+bin/groupBy
+bin/intersectBed
+bin/linksBed
+bin/mapBed
+bin/maskFastaFromBed
+bin/mergeBed
+bin/multiBamCov
+bin/multiIntersectBed
+bin/nucBed
+bin/pairToBed
+bin/pairToPair
+bin/randomBed
+bin/shuffleBed
+bin/slopBed
+bin/sortBed
+bin/subtractBed
+bin/tagBam
+bin/unionBedGraphs
+bin/windowBed
+bin/windowMaker
diff --git a/bedtools2/TODO b/bedtools2/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/bedtools2/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/bedtools2/distinfo b/bedtools2/distinfo
new file mode 100644
index 0000000..d03ce6a
--- /dev/null
+++ b/bedtools2/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (bedtools2-2.23.0.tar.gz) = 7618000d534816cf54983eac39e0eb8f93f9e204
+RMD160 (bedtools2-2.23.0.tar.gz) = 3859e3b92d90b6120d2be808e46158ac51019dbf
+SHA512 (bedtools2-2.23.0.tar.gz) = 1896d567c7e299e032ff7b37a7612875ec99ef78c4b7cb09d4bf4f1b082b3304e0b36aa1cffc4d89d0ae43b3f6b9c0946bcf4d2d049e107055f061c8a42a6dbd
+Size (bedtools2-2.23.0.tar.gz) = 18401280 bytes
+SHA1 (patch-Makefile) = f37141441139fa9b520daa4c26ac87566e047f66
diff --git a/bedtools2/patches/patch-Makefile b/bedtools2/patches/patch-Makefile
new file mode 100644
index 0000000..9d0a58b
--- /dev/null
+++ b/bedtools2/patches/patch-Makefile
@@ -0,0 +1,66 @@
+$NetBSD$
+
+--- Makefile.orig	2015-02-22 22:33:17.000000000 +0000
++++ Makefile
+@@ -4,7 +4,7 @@
+ # (c) 2009 Aaron Quinlan
+ # ==========================
+ 
+-SHELL := /bin/bash -e
++SHELL := /bin/sh -e
+ 
+ VERSION_FILE=./src/utils/version/version_git.h
+ RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
+@@ -12,20 +12,21 @@ RELEASED_VERSION_FILE=./src/utils/versio
+ 
+ 
+ # define our object and binary directories
+-export OBJ_DIR	= obj
+-export BIN_DIR	= bin
+-export SRC_DIR	= src
+-export UTIL_DIR	= src/utils
+-export CXX		= g++
++OBJ_DIR	= obj
++BIN_DIR	= bin
++SRC_DIR	= src
++UTIL_DIR	= src/utils
++CXX		?= g++
+ #ifeq ($(DEBUG),1)
+-#export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
++#CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
+ #else
+-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
++CXXFLAGS ?= -Wall -O2
++CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+ #endif
+-export LIBS		= -lz
+-export BT_ROOT  = src/utils/BamTools/
++LIBS		= -lz
++BT_ROOT  = src/utils/BamTools/
+ 
+-prefix = /usr/local
++PREFIX ?= /usr/local
+ 
+ SUBDIRS = $(SRC_DIR)/annotateBed \
+ 		  $(SRC_DIR)/bamToBed \
+@@ -105,7 +106,7 @@ all: print_banner $(OBJ_DIR) $(BIN_DIR) 
+ 	@echo "done."
+ 	
+ 	@echo "- Creating executables for old CLI."
+-	@python scripts/makeBashScripts.py
++	@${PYTHONBIN} scripts/makeBashScripts.py
+ 	@chmod +x bin/*
+ 	@echo "done."
+ 	
+@@ -113,9 +114,9 @@ all: print_banner $(OBJ_DIR) $(BIN_DIR) 
+ .PHONY: all
+ 
+ install: all
+-	mkdir -p $(DESTDIR)$(prefix)/bin
++	mkdir -p $(DESTDIR)$(PREFIX)/bin
+ 	for file in bin/* ; do \
+-		cp -f $$file $(DESTDIR)$(prefix)/bin; \
++		cp -f $$file $(DESTDIR)$(PREFIX)/bin; \
+ 	done
+ 
+ print_banner:
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