bedtools2: Upgrade to latest release

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: bedtools2: Upgrade to latest release
From: root <root%centosdev.ceas.uwm.edu@localhost>
Date: Thu, 22 Mar 2018 23:16:16 +0000
Module Name:	pkgsrc-wip
Committed By:	root <root%centosdev.ceas.uwm.edu@localhost>
Pushed By:	outpaddling
Date:		Thu Mar 22 18:16:16 2018 -0500
Changeset:	b8164840020d4f748bd7b7c026325e576f2d102a

Modified Files:
	bedtools2/DESCR
	bedtools2/Makefile
	bedtools2/PLIST
	bedtools2/distinfo
	bedtools2/patches/patch-Makefile

Log Message:
bedtools2: Upgrade to latest release

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=b8164840020d4f748bd7b7c026325e576f2d102a

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

diffstat:
 bedtools2/DESCR                  | 11 ++++----
 bedtools2/Makefile               | 29 +++++++++++----------
 bedtools2/PLIST                  |  1 +
 bedtools2/distinfo               | 10 +++----
 bedtools2/patches/patch-Makefile | 56 ++++++++++++++++++----------------------
 5 files changed, 51 insertions(+), 56 deletions(-)

diffs:
diff --git a/bedtools2/DESCR b/bedtools2/DESCR
index 06e818953b..34d2644fb8 100644
--- a/bedtools2/DESCR
+++ b/bedtools2/DESCR
@@ -1,7 +1,6 @@
-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 
+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
index fb212e5c6c..9375a173dc 100644
--- a/bedtools2/Makefile
+++ b/bedtools2/Makefile
@@ -4,34 +4,35 @@
 #               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=	bacon%NetBSD.org@localhost
-HOMEPAGE=	
+HOMEPAGE=	https://github.com/arq5x/bedtools2
 COMMENT=	Swiss army knife for genome arithmetic
 LICENSE=	gnu-gpl-v2
 
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	gmake
+REPLACE_BASH=	scripts/*.sh
+REPLACE_PYTHON=	scripts/*.py
+
+# WRKSRC=		${WRKDIR}/bedtools2-${PORTVERSION}
+
+# MAKE_ENV=	PYTHONBIN=${PYTHONBIN}
+
+PORTVERSION=	2.27.1
 
-WRKSRC=		${WRKDIR}/bedtools2-${PORTVERSION}
+.include "../../mk/bsd.prefs.mk"
 
-MAKE_ENV=	PYTHONBIN=${PYTHONBIN}
+.if ${MACHINE_ARCH} == i386
+MAKE_ENV+=	POPCNT_CAPABILITY=0
+.endif
 
-PORTVERSION=	2.23.0
+post-install:
+	${STRIP_CMD} ${DESTDIR}${PREFIX}/bin/bedtools
 
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../lang/python/application.mk"
diff --git a/bedtools2/PLIST b/bedtools2/PLIST
index 785ac67498..7902461b1a 100644
--- a/bedtools2/PLIST
+++ b/bedtools2/PLIST
@@ -28,6 +28,7 @@ bin/nucBed
 bin/pairToBed
 bin/pairToPair
 bin/randomBed
+bin/shiftBed
 bin/shuffleBed
 bin/slopBed
 bin/sortBed
diff --git a/bedtools2/distinfo b/bedtools2/distinfo
index d03ce6ae75..b106a62860 100644
--- a/bedtools2/distinfo
+++ b/bedtools2/distinfo
@@ -1,7 +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
+SHA1 (bedtools2-2.27.1.tar.gz) = 0f45ade764913f88b332c3126f152fd55da9a101
+RMD160 (bedtools2-2.27.1.tar.gz) = 957b40f240fd6b22374165f25b96fc4aa3fb8f5a
+SHA512 (bedtools2-2.27.1.tar.gz) = 65d58b5d9e00581ed73f2d5a58be56c888adbc4045396e62fe39abc27a2abcd974721c7fe25533d76613788e43529b5df427ad19acce7ff6e7133018cdd35f40
+Size (bedtools2-2.27.1.tar.gz) = 20003119 bytes
+SHA1 (patch-Makefile) = 4058adb49f01b5e643349f06f53fc247a2014b42
diff --git a/bedtools2/patches/patch-Makefile b/bedtools2/patches/patch-Makefile
index 9d0a58b71d..c6d3004772 100644
--- a/bedtools2/patches/patch-Makefile
+++ b/bedtools2/patches/patch-Makefile
@@ -1,6 +1,8 @@
 $NetBSD$
 
---- Makefile.orig	2015-02-22 22:33:17.000000000 +0000
+# Use portable shell path, respect env
+
+--- Makefile.orig	2018-03-22 23:06:52.521063536 +0000
 +++ Makefile
 @@ -4,7 +4,7 @@
  # (c) 2009 Aaron Quinlan
@@ -11,48 +13,40 @@ $NetBSD$
  
  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
+@@ -16,11 +16,11 @@ 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 ($(DEBUG),1)
--#export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
-+#CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
- #else
++export CXX		?= g++
+ ifeq ($(DEBUG),1)
+-export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
++#export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+ 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/
++export CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+ endif
  
--prefix = /usr/local
+ # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
+@@ -33,7 +33,7 @@ endif
+ export LIBS		= -lz
+ export 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) 
+@@ -148,7 +148,7 @@ all: print_banner $(OBJ_DIR) $(BIN_DIR)
  	@echo "done."
- 	
+ 
  	@echo "- Creating executables for old CLI."
 -	@python scripts/makeBashScripts.py
-+	@${PYTHONBIN} scripts/makeBashScripts.py
++	scripts/makeBashScripts.py
  	@chmod +x bin/*
  	@echo "done."
- 	
-@@ -113,9 +114,9 @@ all: print_banner $(OBJ_DIR) $(BIN_DIR) 
+ 
+@@ -156,9 +156,9 @@ all: print_banner $(OBJ_DIR) $(BIN_DIR)
  .PHONY: all
  
  install: all
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