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locks; strict;
comment	@# @;


1.3
date	2023.11.08.16.46.44;	author bacon;	state Exp;
branches;
next	1.2;
commitid	MORyswU6I0JRkPLE;

1.2
date	2021.02.08.01.49.25;	author bacon;	state Exp;
branches;
next	1.1;
commitid	LeuJXahXgOf3BQGC;

1.1
date	2021.01.22.17.07.50;	author bacon;	state Exp;
branches;
next	;
commitid	p2JteL9RJEs1fKEC;


desc
@@


1.3
log
@biology/bedtools: Update to 2.31.1

Code updates for modern compilers

Changes: https://github.com/arq5x/bedtools2/releases
@
text
@$NetBSD$

# Portability, respect env

--- Makefile.orig	2023-11-08 15:05:30.454330622 +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++
 
 PYTHON ?= $(shell python --version >/dev/null 2>&1 && echo "python" || echo python3)
 
@@@@ -43,7 +43,7 @@@@ endif
 BT_LDFLAGS =
 BT_LIBS    = -lz -lm -lbz2 -llzma -lpthread
 
-prefix ?= /usr/local
+PREFIX ?= /usr/local
 
 SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/bamToBed \
@@@@ -158,7 +158,7 @@@@ $(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_C
 @@mv -f $*.Td $*.d
 endef
 
-$(OBJ_DIR)/%.d: ;
+$(OBJ_DIR)/%.d: $(OBJ_DIR);
 .PRECIOUS: $(OBJ_DIR)/%.d
 
 -include $(patsubst %.o,%.d,$(BUILT_OBJECTS))
@@@@ -200,9 +200,9 @@@@ $(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:
@


1.2
log
@biology/bedtools: Update to 2.30.0

Some major performance improvements
Numerous minor bug fixes and enhancements
Added a do-test target to the pkgsrc Makefile
@
text
@d3 1
a3 1
# Respect pkgsrc env, drop bash dep
d5 1
a5 1
--- Makefile.orig	2021-02-05 21:42:03.926301547 +0000
d23 3
a25 3
 ifeq ($(DEBUG),1)
 BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
@@@@ -41,7 +41,7 @@@@ endif
d34 1
a34 1
@@@@ -155,7 +155,7 @@@@ $(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_C
d39 1
a39 1
+$(OBJ_DIR)/%.d: $(OBJ_DIR) ;
d43 1
a43 1
@@@@ -197,9 +197,9 @@@@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
@


1.1
log
@biology/bedtools: import bedtools-2.29.2

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.
@
text
@d5 1
a5 1
--- Makefile.orig	2019-12-17 20:12:15.000000000 +0000
d34 10
a43 1
@@@@ -191,9 +191,9 @@@@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
@