bedtools: Clean up Makefile and patches

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Feb 5 15:17:16 2021 -0600
Changeset:	f4d822e0231a42758d24285bdfaf59ca16004127

Modified Files:
	bedtools/Makefile
	bedtools/distinfo
	bedtools/patches/patch-Makefile
	bedtools/patches/patch-src_utils_htslib_Makefile

Log Message:
bedtools: Clean up Makefile and patches

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f4d822e0231a42758d24285bdfaf59ca16004127

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

diffstat:
 bedtools/Makefile                                |  4 +---
 bedtools/distinfo                                |  4 ++--
 bedtools/patches/patch-Makefile                  | 22 ++++++++++++++++++++--
 bedtools/patches/patch-src_utils_htslib_Makefile |  2 +-
 4 files changed, 24 insertions(+), 8 deletions(-)

diffs:
diff --git a/bedtools/Makefile b/bedtools/Makefile
index 3dd0debc50..6ad5757e4c 100644
--- a/bedtools/Makefile
+++ b/bedtools/Makefile
@@ -11,10 +11,8 @@ HOMEPAGE=	https://bedtools.readthedocs.io/en/latest/
 COMMENT=	Swiss army knife for genome arithmetic
 LICENSE=	mit
 
-TEST_DEPENDS+=	bash
-
 USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake
+USE_TOOLS+=	bash:test gmake
 REPLACE_SH+=	scripts/vcfsort.sh
 REPLACE_PYTHON=	scripts/makeBashScripts.py
 
diff --git a/bedtools/distinfo b/bedtools/distinfo
index 1c7a14939b..2711eaa0fa 100644
--- a/bedtools/distinfo
+++ b/bedtools/distinfo
@@ -4,6 +4,6 @@ SHA1 (bedtools-2.30.0.tar.gz) = b3bae21434f261818e15875727b4a3c5c7366bc7
 RMD160 (bedtools-2.30.0.tar.gz) = 1cc30e5bc3df12f38d8f1e055ff2f939d7608395
 SHA512 (bedtools-2.30.0.tar.gz) = 3d69d6a53d3e5d15597dfefa26f7895231adbf3c1fe3b16ee4213e497ef01a20698add2f0e6f03d8eb7cd7c70709955f0ebdf897a025a83d31ef17e2c91f9856
 Size (bedtools-2.30.0.tar.gz) = 20639858 bytes
-SHA1 (patch-Makefile) = d6a76cb23e623842d6d5c60d67eff928b45b091c
+SHA1 (patch-Makefile) = 0cbebf2830ec526b390f05baa54baee7f54d73c5
 SHA1 (patch-src_utils_BamTools_include_SamHeader.hpp) = 7ab168b247b5edf7f3eccd9ef7329a5e1605c787
-SHA1 (patch-src_utils_htslib_Makefile) = ba513efa59eed05321c176185fb576f4892ea7a5
+SHA1 (patch-src_utils_htslib_Makefile) = 8785ff3110f8df26e0cc5b2fdf1e2e02d6cdc836
diff --git a/bedtools/patches/patch-Makefile b/bedtools/patches/patch-Makefile
index 8c8c19dd3e..ac23131a6c 100644
--- a/bedtools/patches/patch-Makefile
+++ b/bedtools/patches/patch-Makefile
@@ -2,7 +2,7 @@ $NetBSD$
 
 # Respect pkgsrc env, drop bash dep
 
---- Makefile.orig	2019-12-17 20:12:15.000000000 +0000
+--- Makefile.orig	2021-01-23 19:33:26.000000000 +0000
 +++ Makefile
 @@ -4,7 +4,7 @@
  # (c) 2009 Aaron Quinlan
@@ -31,7 +31,25 @@ $NetBSD$
  
  SUBDIRS = $(SRC_DIR)/annotateBed \
  		  $(SRC_DIR)/bamToBed \
-@@ -191,9 +191,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
+@@ -155,7 +155,7 @@ $(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))
+@@ -189,7 +189,7 @@ test/htsutil: $(OBJ_DIR)/htsutil.o $(HTS
+ 
+ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
+ 	@echo "- Creating executables for old CLI."
+-	@python scripts/makeBashScripts.py
++	@/Users/bacon/Pkgsrc/pkg/bin//Users/bacon/Pkgsrc/pkg/bin/python3.83.8 scripts/makeBashScripts.py
+ 	@chmod +x bin/*
+ 	@echo "done."
+ 
+@@ -197,9 +197,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
  .PHONY: all
  
  install: all
diff --git a/bedtools/patches/patch-src_utils_htslib_Makefile b/bedtools/patches/patch-src_utils_htslib_Makefile
index 3de50d71c5..17e208e4e2 100644
--- a/bedtools/patches/patch-src_utils_htslib_Makefile
+++ b/bedtools/patches/patch-src_utils_htslib_Makefile
@@ -2,7 +2,7 @@ $NetBSD$
 
 # Respect pkgsrc env
 
---- src/utils/htslib/Makefile.orig	2021-01-21 22:49:18.823750624 +0000
+--- src/utils/htslib/Makefile.orig	2021-01-23 19:33:26.000000000 +0000
 +++ src/utils/htslib/Makefile
 @@ -22,7 +22,7 @@
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER