svn commit: r511958 - in head/biology/bedtools: . files
Jason W. Bacon
jwb at FreeBSD.org
Fri Sep 13 13:22:00 UTC 2019
Author: jwb
Date: Fri Sep 13 13:21:59 2019
New Revision: 511958
URL: https://svnweb.freebsd.org/changeset/ports/511958
Log:
biology/bedtools: Upgrade to 2.29.0
Add test target to run test scripts in dist
Reported by: portscout
Added:
head/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h (contents, props changed)
head/biology/bedtools/files/patch-src_utils_htslib_Makefile (contents, props changed)
Modified:
head/biology/bedtools/Makefile
head/biology/bedtools/distinfo
head/biology/bedtools/files/patch-Makefile
Modified: head/biology/bedtools/Makefile
==============================================================================
--- head/biology/bedtools/Makefile Fri Sep 13 13:17:26 2019 (r511957)
+++ head/biology/bedtools/Makefile Fri Sep 13 13:21:59 2019 (r511958)
@@ -1,10 +1,9 @@
# $FreeBSD$
-PORTNAME= bedtools
+PORTNAME= bedtools
DISTVERSIONPREFIX= v
-DISTVERSION= 2.27.1
-PORTREVISION= 3
-CATEGORIES= biology
+DISTVERSION= 2.29.0
+CATEGORIES= biology
MAINTAINER= jwb at FreeBSD.org
COMMENT= Toolset for genome set arithmetic such as intersect, union
@@ -12,6 +11,8 @@ COMMENT= Toolset for genome set arithmetic such as int
LICENSE= GPLv2
LICENSE_FILE= ${WRKSRC}/LICENSE
+TEST_DEPENDS= bash:shells/bash
+
USES= compiler:c++11-lang gmake python
USE_GITHUB= yes
GH_ACCOUNT= arq5x
@@ -22,15 +23,17 @@ post-extract:
@${MV} ${WRKSRC}/src/utils/gzstream/version \
${WRKSRC}/src/utils/gzstream/version.txt
-pre-build:
+pre-configure:
@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' ${WRKSRC}/Makefile
@${REINPLACE_CMD} -e 's|@\$$(CXX)|$$(CXX)|g' \
${WRKSRC}/*/Makefile \
${WRKSRC}/*/*/Makefile \
- ${WRKSRC}/*/*/*/Makefile \
- ${WRKSRC}/*/*/*/*/Makefile
+ ${WRKSRC}/*/*/*/Makefile
post-install:
${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/bedtools
+
+do-test:
+ (cd ${WRKSRC}/test && bash test.sh)
.include <bsd.port.mk>
Modified: head/biology/bedtools/distinfo
==============================================================================
--- head/biology/bedtools/distinfo Fri Sep 13 13:17:26 2019 (r511957)
+++ head/biology/bedtools/distinfo Fri Sep 13 13:21:59 2019 (r511958)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1519746174
-SHA256 (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112
-SIZE (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = 20003119
+TIMESTAMP = 1567891084
+SHA256 (arq5x-bedtools2-v2.29.0_GH0.tar.gz) = 8a13b7ec93a2dc960616268d8009f6061bec5a32b8a38d5734f80e851bb8ed1e
+SIZE (arq5x-bedtools2-v2.29.0_GH0.tar.gz) = 20635364
Modified: head/biology/bedtools/files/patch-Makefile
==============================================================================
--- head/biology/bedtools/files/patch-Makefile Fri Sep 13 13:17:26 2019 (r511957)
+++ head/biology/bedtools/files/patch-Makefile Fri Sep 13 13:21:59 2019 (r511958)
@@ -1,4 +1,4 @@
---- Makefile.orig 2017-12-14 17:15:02 UTC
+--- Makefile.orig 2019-09-07 21:14:56 UTC
+++ Makefile
@@ -4,7 +4,7 @@
# (c) 2009 Aaron Quinlan
@@ -9,42 +9,25 @@
VERSION_FILE=./src/utils/version/version_git.h
RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
-@@ -16,11 +16,11 @@ export OBJ_DIR = obj
- export BIN_DIR = bin
- export SRC_DIR = src
- export UTIL_DIR = src/utils
--export CXX = g++
-+export CXX ?= g++
- ifeq ($(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)
-+export CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
- endif
+@@ -20,7 +20,7 @@ OBJ_DIR = obj
+ BIN_DIR = bin
+ SRC_DIR = src
- # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
-@@ -33,7 +33,7 @@ endif
- export LIBS = -lz
- export BT_ROOT = src/utils/BamTools/
+-CXX = g++
++CXX ?= g++
+ ifeq ($(DEBUG),1)
+ BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+@@ -40,7 +40,7 @@ endif
+ BT_LDFLAGS =
+ BT_LIBS = -lz -lm -lbz2 -llzma -lpthread
+
-prefix ?= /usr/local
+PREFIX ?= /usr/local
SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/bamToBed \
-@@ -143,8 +143,8 @@ INCLUDES = -I$(SRC_DIR)/utils/bedFile \
-
- all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
- @echo "- Building main bedtools binary."
-- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
-- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
- @echo "done."
-
- @echo "- Creating executables for old CLI."
-@@ -156,9 +156,9 @@ all: print_banner $(OBJ_DIR) $(BIN_DIR)
+@@ -183,9 +183,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
.PHONY: all
install: all
@@ -56,12 +39,3 @@
done
print_banner:
-@@ -193,7 +193,7 @@ clean:
- .PHONY: clean
-
- test: all
-- @cd test; bash test.sh
-+ @cd test; $(SHELL) test.sh
-
- .PHONY: test
-
Added: head/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h Fri Sep 13 13:21:59 2019 (r511958)
@@ -0,0 +1,11 @@
+--- src/utils/Contexts/ContextBase.h.orig 2019-03-25 18:03:45 UTC
++++ src/utils/Contexts/ContextBase.h
+@@ -44,7 +44,7 @@ public:
+ FileRecordMgr *getFile(int fileIdx) { return _files[fileIdx]; }
+ void setProgram(PROGRAM_TYPE program) { _program = program; }
+
+- void addInputFile(const string &inputFile) { _fileNames.push_back(inputFile); }
++ void addInputFile(const string &inputFile) { _fileNames.push_back(inputFile); cerr << "Adding " << inputFile << endl; }
+
+ int getNumInputFiles() const { return _fileNames.size(); }
+ const string &getInputFileName(int fileNum) const { return _fileNames[fileNum]; }
Added: head/biology/bedtools/files/patch-src_utils_htslib_Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bedtools/files/patch-src_utils_htslib_Makefile Fri Sep 13 13:21:59 2019 (r511958)
@@ -0,0 +1,27 @@
+--- src/utils/htslib/Makefile.orig 2019-03-25 03:58:18 UTC
++++ src/utils/htslib/Makefile
+@@ -22,9 +22,9 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+
+-CC = gcc
+-AR = ar
+-RANLIB = ranlib
++CC ?= gcc
++AR ?= ar
++RANLIB ?= ranlib
+
+ # Default libraries to link if configure is not used
+ htslib_default_libs = -lz -lm -lbz2 -llzma
+@@ -33,9 +33,9 @@ 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 =
++LDFLAGS ?=
+ LIBS = $(htslib_default_libs)
+
+ prefix = /usr/local
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