bedtools2: Rename to bedtools and fix script name

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: bedtools2: Rename to bedtools and fix script name
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Fri, 22 Jan 2021 17:00:57 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Jan 22 11:00:57 2021 -0600
Changeset:	dc1a778dc70d599b69005146c2a3b0ca01465a6e

Added Files:
	bedtools/DESCR
	bedtools/Makefile
	bedtools/PLIST
	bedtools/distinfo
	bedtools/patches/patch-Makefile
	bedtools/patches/patch-src_utils_htslib_Makefile
Removed Files:
	bedtools2/DESCR
	bedtools2/Makefile
	bedtools2/PLIST
	bedtools2/distinfo
	bedtools2/patches/patch-Makefile
	bedtools2/patches/patch-src_utils_htslib_Makefile

Log Message:
bedtools2: Rename to bedtools and fix script name

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=dc1a778dc70d599b69005146c2a3b0ca01465a6e

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

diffstat:
 bedtools/DESCR                                    | 10 +++++
 bedtools/Makefile                                 | 33 +++++++++++++++++
 bedtools/PLIST                                    | 39 ++++++++++++++++++++
 bedtools/distinfo                                 |  8 ++++
 bedtools/patches/patch-Makefile                   | 45 +++++++++++++++++++++++
 bedtools/patches/patch-src_utils_htslib_Makefile  | 24 ++++++++++++
 bedtools2/DESCR                                   | 10 -----
 bedtools2/Makefile                                | 33 -----------------
 bedtools2/PLIST                                   | 39 --------------------
 bedtools2/distinfo                                |  8 ----
 bedtools2/patches/patch-Makefile                  | 45 -----------------------
 bedtools2/patches/patch-src_utils_htslib_Makefile | 24 ------------
 12 files changed, 159 insertions(+), 159 deletions(-)

diffs:
diff --git a/bedtools/DESCR b/bedtools/DESCR
new file mode 100644
index 0000000000..bf60338ab7
--- /dev/null
+++ b/bedtools/DESCR
@@ -0,0 +1,10 @@
+The bedtools utilities are a suite of tools for performing a wide range of
+genomics analysis tasks.  The most widely-used of these tools enable genome
+arithmetic, i.e., set theory on the genome.  For example, with bedtools one
+can intersect, merge, count, complement, and shuffle genomic intervals from
+multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
+
+Although each individual utility is designed to do a relatively simple task,
+e.g., intersect two interval files, more sophisticated analyses can be
+conducted by stringing together multiple bedtools operations on the command
+line or in shell scripts.
diff --git a/bedtools/Makefile b/bedtools/Makefile
new file mode 100644
index 0000000000..b1bc0d6554
--- /dev/null
+++ b/bedtools/Makefile
@@ -0,0 +1,33 @@
+# $NetBSD$
+
+DISTNAME=	bedtools-2.29.2
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=arq5x/}
+GITHUB_PROJECT=	bedtools2
+GITHUB_TAG=	v${PKGVERSION_NOREV}
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	https://bedtools.readthedocs.io/en/latest/
+COMMENT=	Swiss army knife for genome arithmetic
+LICENSE=	mit
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+REPLACE_SH+=	scripts/vcfsort.sh
+REPLACE_PYTHON=	scripts/makeBashScripts.py
+
+SUBST_CLASSES+=		pybin
+SUBST_STAGE.pybin=	pre-configure
+SUBST_SED.pybin=	-e 's|python|${PYTHONBIN}|g'
+SUBST_FILES.pybin=	Makefile
+
+# Avoid conflict with C++20 <version> by adding .txt suffix
+post-extract:
+	${MV} ${WRKSRC}/src/utils/gzstream/version \
+		${WRKSRC}/src/utils/gzstream/version.txt
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/xz/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/bedtools/PLIST b/bedtools/PLIST
new file mode 100644
index 0000000000..7902461b1a
--- /dev/null
+++ b/bedtools/PLIST
@@ -0,0 +1,39 @@
+@comment $NetBSD$
+bin/annotateBed
+bin/bamToBed
+bin/bamToFastq
+bin/bed12ToBed6
+bin/bedToBam
+bin/bedToIgv
+bin/bedpeToBam
+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/shiftBed
+bin/shuffleBed
+bin/slopBed
+bin/sortBed
+bin/subtractBed
+bin/tagBam
+bin/unionBedGraphs
+bin/windowBed
+bin/windowMaker
diff --git a/bedtools/distinfo b/bedtools/distinfo
new file mode 100644
index 0000000000..17501fd9cb
--- /dev/null
+++ b/bedtools/distinfo
@@ -0,0 +1,8 @@
+$NetBSD$
+
+SHA1 (bedtools-2.29.2.tar.gz) = 51f03e1cac60f99c062d9babb6385800c89c78f6
+RMD160 (bedtools-2.29.2.tar.gz) = 08ea14501ddfc85f2d4a5a756a10512a61ec93f2
+SHA512 (bedtools-2.29.2.tar.gz) = 06b0016674acb08fd85b80fe1a8ff1ebce5c54c0a30ff7f4e52e63fe5b3f3841413f49df3c51088454d79048ca267fde8c23d9ed51f309ee6916d9b49610be41
+Size (bedtools-2.29.2.tar.gz) = 20638840 bytes
+SHA1 (patch-Makefile) = d6a76cb23e623842d6d5c60d67eff928b45b091c
+SHA1 (patch-src_utils_htslib_Makefile) = ba513efa59eed05321c176185fb576f4892ea7a5
diff --git a/bedtools/patches/patch-Makefile b/bedtools/patches/patch-Makefile
new file mode 100644
index 0000000000..8c8c19dd3e
--- /dev/null
+++ b/bedtools/patches/patch-Makefile
@@ -0,0 +1,45 @@
+$NetBSD$
+
+# Respect pkgsrc env, drop bash dep
+
+--- Makefile.orig	2019-12-17 20:12:15.000000000 +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
+@@ -21,7 +21,7 @@ OBJ_DIR	= obj
+ BIN_DIR	= bin
+ SRC_DIR	= src
+ 
+-CXX     = g++
++CXX     ?= g++
+ 
+ ifeq ($(DEBUG),1)
+ BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+@@ -41,7 +41,7 @@ endif
+ BT_LDFLAGS =
+ BT_LIBS    = -lz -lm -lbz2 -llzma -lpthread
+ 
+-prefix ?= /usr/local
++PREFIX ?= /usr/local
+ 
+ SUBDIRS = $(SRC_DIR)/annotateBed \
+ 		  $(SRC_DIR)/bamToBed \
+@@ -191,9 +191,9 @@ $(BIN_DIR)/intersectBed: | $(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:
diff --git a/bedtools/patches/patch-src_utils_htslib_Makefile b/bedtools/patches/patch-src_utils_htslib_Makefile
new file mode 100644
index 0000000000..3de50d71c5
--- /dev/null
+++ b/bedtools/patches/patch-src_utils_htslib_Makefile
@@ -0,0 +1,24 @@
+$NetBSD$
+
+# Respect pkgsrc env
+
+--- src/utils/htslib/Makefile.orig	2021-01-21 22:49:18.823750624 +0000
++++ src/utils/htslib/Makefile
+@@ -22,7 +22,7 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC     = gcc
++CC     ?= gcc
+ AR     = ar
+ RANLIB = ranlib
+ 
+@@ -33,7 +33,7 @@ CPPFLAGS =
+ # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+ # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
+ #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
+-CFLAGS   = -g -Wall -O2
++CFLAGS   ?= -g -Wall -O2
+ EXTRA_CFLAGS_PIC = -fpic
+ LDFLAGS  =
+ LIBS     = $(htslib_default_libs)
diff --git a/bedtools2/DESCR b/bedtools2/DESCR
deleted file mode 100644
index bf60338ab7..0000000000
--- a/bedtools2/DESCR
+++ /dev/null
@@ -1,10 +0,0 @@
-The bedtools utilities are a suite of tools for performing a wide range of
-genomics analysis tasks.  The most widely-used of these tools enable genome
-arithmetic, i.e., set theory on the genome.  For example, with bedtools one
-can intersect, merge, count, complement, and shuffle genomic intervals from
-multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
-
-Although each individual utility is designed to do a relatively simple task,
-e.g., intersect two interval files, more sophisticated analyses can be
-conducted by stringing together multiple bedtools operations on the command
-line or in shell scripts.
diff --git a/bedtools2/Makefile b/bedtools2/Makefile
deleted file mode 100644
index 6b06e04a06..0000000000
--- a/bedtools2/Makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	bedtools-2.29.2
-CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=arq5x/}
-GITHUB_PROJECT=	bedtools2
-GITHUB_TAG=	v${PKGVERSION_NOREV}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://bedtools.readthedocs.io/en/latest/
-COMMENT=	Swiss army knife for genome arithmetic
-LICENSE=	mit
-
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake
-REPLACE_SH+=	scripts/vcfsortsh.sh
-REPLACE_PYTHON=	scripts/makeBashScripts.py
-
-SUBST_CLASSES+=		pybin
-SUBST_STAGE.pybin=	pre-configure
-SUBST_SED.pybin=	-e 's|python|${PYTHONBIN}|g'
-SUBST_FILES.pybin=	Makefile
-
-# Avoid conflict with C++20 <version> by adding .txt suffix
-post-extract:
-	${MV} ${WRKSRC}/src/utils/gzstream/version \
-		${WRKSRC}/src/utils/gzstream/version.txt
-
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../archivers/bzip2/buildlink3.mk"
-.include "../../archivers/xz/buildlink3.mk"
-.include "../../lang/python/application.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/bedtools2/PLIST b/bedtools2/PLIST
deleted file mode 100644
index 7902461b1a..0000000000
--- a/bedtools2/PLIST
+++ /dev/null
@@ -1,39 +0,0 @@
-@comment $NetBSD$
-bin/annotateBed
-bin/bamToBed
-bin/bamToFastq
-bin/bed12ToBed6
-bin/bedToBam
-bin/bedToIgv
-bin/bedpeToBam
-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/shiftBed
-bin/shuffleBed
-bin/slopBed
-bin/sortBed
-bin/subtractBed
-bin/tagBam
-bin/unionBedGraphs
-bin/windowBed
-bin/windowMaker
diff --git a/bedtools2/distinfo b/bedtools2/distinfo
deleted file mode 100644
index 17501fd9cb..0000000000
--- a/bedtools2/distinfo
+++ /dev/null
@@ -1,8 +0,0 @@
-$NetBSD$
-
-SHA1 (bedtools-2.29.2.tar.gz) = 51f03e1cac60f99c062d9babb6385800c89c78f6
-RMD160 (bedtools-2.29.2.tar.gz) = 08ea14501ddfc85f2d4a5a756a10512a61ec93f2
-SHA512 (bedtools-2.29.2.tar.gz) = 06b0016674acb08fd85b80fe1a8ff1ebce5c54c0a30ff7f4e52e63fe5b3f3841413f49df3c51088454d79048ca267fde8c23d9ed51f309ee6916d9b49610be41
-Size (bedtools-2.29.2.tar.gz) = 20638840 bytes
-SHA1 (patch-Makefile) = d6a76cb23e623842d6d5c60d67eff928b45b091c
-SHA1 (patch-src_utils_htslib_Makefile) = ba513efa59eed05321c176185fb576f4892ea7a5
diff --git a/bedtools2/patches/patch-Makefile b/bedtools2/patches/patch-Makefile
deleted file mode 100644
index 8c8c19dd3e..0000000000
--- a/bedtools2/patches/patch-Makefile
+++ /dev/null
@@ -1,45 +0,0 @@
-$NetBSD$
-
-# Respect pkgsrc env, drop bash dep
-
---- Makefile.orig	2019-12-17 20:12:15.000000000 +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
-@@ -21,7 +21,7 @@ OBJ_DIR	= obj
- BIN_DIR	= bin
- SRC_DIR	= src
- 
--CXX     = g++
-+CXX     ?= g++
- 
- ifeq ($(DEBUG),1)
- BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
-@@ -41,7 +41,7 @@ endif
- BT_LDFLAGS =
- BT_LIBS    = -lz -lm -lbz2 -llzma -lpthread
- 
--prefix ?= /usr/local
-+PREFIX ?= /usr/local
- 
- SUBDIRS = $(SRC_DIR)/annotateBed \
- 		  $(SRC_DIR)/bamToBed \
-@@ -191,9 +191,9 @@ $(BIN_DIR)/intersectBed: | $(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:
diff --git a/bedtools2/patches/patch-src_utils_htslib_Makefile b/bedtools2/patches/patch-src_utils_htslib_Makefile
deleted file mode 100644
index 3de50d71c5..0000000000
--- a/bedtools2/patches/patch-src_utils_htslib_Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-$NetBSD$
-
-# Respect pkgsrc env
-
---- src/utils/htslib/Makefile.orig	2021-01-21 22:49:18.823750624 +0000
-+++ src/utils/htslib/Makefile
-@@ -22,7 +22,7 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC     = gcc
-+CC     ?= gcc
- AR     = ar
- RANLIB = ranlib
- 
-@@ -33,7 +33,7 @@ CPPFLAGS =
- # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
- # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
- #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
--CFLAGS   = -g -Wall -O2
-+CFLAGS   ?= -g -Wall -O2
- EXTRA_CFLAGS_PIC = -fpic
- LDFLAGS  =
- LIBS     = $(htslib_default_libs)
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