biology/hisat2: Update to 2.2.1

pkgsrc fix: Unbreak build on Darwin

Add python3 support
Several bug fixes and enhancements
Changes: https://github.com/DaehwanKimLab/hisat2/tags


(bacon)

$NetBSD: patch-Makefile,v 1.1 2022/03/17 16:01:12 bacon Exp $

# Respect env

--- Makefile.orig	2020-07-24 20:07:54.000000000 +0000
+++ Makefile
@@ -23,9 +23,11 @@
 INC =
 GCC_PREFIX = $(shell dirname `which gcc`)
 GCC_SUFFIX =
-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
-CXX = $(CPP)
+CC	?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
+CPP	?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
+CXX	?= $(CPP)
+INSTALL	?= install
+
 HEADERS = $(wildcard *.h)
 BOWTIE_MM = 1
 BOWTIE_SHARED_MEM = 0
@@ -55,7 +57,7 @@ ifneq (,$(findstring Darwin,$(shell unam
 	MACOS = 1
 endif
 
-EXTRA_FLAGS += -DPOPCNT_CAPABILITY -std=c++11
+EXTRA_FLAGS += -std=c++11
 INC += -I. -I third_party 
 
 MM_DEF = 
@@ -150,33 +152,11 @@ HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) h
 HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS) hisat2_repeat_main.cpp
 
 SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
-VERSION = $(shell cat VERSION)
-
-# Convert BITS=?? to a -m flag
-BITS=32
-ifeq (x86_64,$(shell uname -m))
-BITS=64
-endif
-# msys will always be 32 bit so look at the cpu arch instead.
-ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
-	ifeq (1,$(MINGW))
-		BITS=64
-	endif
-endif
-BITS_FLAG =
-
-ifeq (32,$(BITS))
-	BITS_FLAG = -m32
-endif
-
-ifeq (64,$(BITS))
-	BITS_FLAG = -m64
-endif
-SSE_FLAG=-msse2
+HISAT2_VERSION = $(shell cat HISAT2_VERSION)
 
 DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
 DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
-RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
+RELEASE_FLAGS  = $(CXXFLAGS)
 RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
 NOASSERT_FLAGS = -DNDEBUG
 FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
@@ -251,7 +231,7 @@ GENERAL_LIST = $(wildcard scripts/*.sh) 
 	MANUAL \
 	MANUAL.markdown \
 	TUTORIAL \
-	VERSION
+	HISAT2_VERSION
 
 ifeq (1,$(WINDOWS))
 	HISAT2_BIN_LIST := $(HISAT2_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat 
@@ -287,7 +267,7 @@ repeat: hisat2-repeat
 repeat-debug: hisat2-repeat-debug
 
 DEFS=-fno-strict-aliasing \
-     -DHISAT2_VERSION="\"`cat VERSION`\"" \
+     -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" \
      -DBUILD_HOST="\"`hostname`\"" \
      -DBUILD_TIME="\"`date`\"" \
      -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
@@ -517,12 +497,12 @@ hisat2-inspect.bat:
 hisat2-src: $(SRC_PKG_LIST)
 	chmod a+x scripts/*.sh scripts/*.pl
 	mkdir .src.tmp
-	mkdir .src.tmp/hisat2-$(VERSION)
+	mkdir .src.tmp/hisat2-$(HISAT2_VERSION)
 	zip tmp.zip $(SRC_PKG_LIST)
-	mv tmp.zip .src.tmp/hisat2-$(VERSION)
-	cd .src.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
-	cd .src.tmp ; zip -r hisat2-$(VERSION)-source.zip hisat2-$(VERSION)
-	cp .src.tmp/hisat2-$(VERSION)-source.zip .
+	mv tmp.zip .src.tmp/hisat2-$(HISAT2_VERSION)
+	cd .src.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip
+	cd .src.tmp ; zip -r hisat2-$(HISAT2_VERSION)-source.zip hisat2-$(HISAT2_VERSION)
+	cp .src.tmp/hisat2-$(HISAT2_VERSION)-source.zip .
 	rm -rf .src.tmp
 
 .PHONY: hisat2-bin
@@ -530,16 +510,16 @@ hisat2-bin: $(BIN_PKG_LIST) $(HISAT2_BIN
 	chmod a+x scripts/*.sh scripts/*.pl
 	rm -rf .bin.tmp
 	mkdir .bin.tmp
-	mkdir .bin.tmp/hisat2-$(VERSION)
+	mkdir .bin.tmp/hisat2-$(HISAT2_VERSION)
 	if [ -f hisat2.exe ] ; then \
 		zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) ; \
 	else \
 		zip tmp.zip $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) ; \
 	fi
-	mv tmp.zip .bin.tmp/hisat2-$(VERSION)
-	cd .bin.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
-	cd .bin.tmp ; zip -r hisat2-$(VERSION)-$(BITS).zip hisat2-$(VERSION)
-	cp .bin.tmp/hisat2-$(VERSION)-$(BITS).zip .
+	mv tmp.zip .bin.tmp/hisat2-$(HISAT2_VERSION)
+	cd .bin.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip
+	cd .bin.tmp ; zip -r hisat2-$(HISAT2_VERSION)-$(BITS).zip hisat2-$(HISAT2_VERSION)
+	cp .bin.tmp/hisat2-$(HISAT2_VERSION)-$(BITS).zip .
 	rm -rf .bin.tmp
 
 .PHONY: doc
@@ -554,6 +534,20 @@ doc/manual.inc.html: MANUAL.markdown
 MANUAL: MANUAL.markdown
 	perl doc/strip_markdown.pl < $^ > $@
 
+# Install per filesystem hierarchy standard:
+# https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
+
+.PHONY: install
+install:
+	mkdir -p ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -c -s ${HISAT2_BIN_LIST} ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -c hisat2 hisat2-build hisat2-inspect \
+		${DESTDIR}${PREFIX}/bin
+
+	mkdir -p ${DESTDIR}${PREFIX}/libexec/hisat2
+	${INSTALL} -c scripts/*.sh scripts/*.pl scripts/*.py *.py \
+		${DESTDIR}${PREFIX}/libexec/hisat2
+
 .PHONY: clean
 clean:
 	rm -f $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) \

$NetBSD: patch-processor__support.h,v 1.1 2022/03/17 16:01:12 bacon Exp $

# Support non-x86

--- processor_support.h.orig	2020-07-24 20:07:54 UTC
+++ processor_support.h
@@ -12,7 +12,7 @@
 
 #if defined(__INTEL_COMPILER)
 #   define USING_INTEL_COMPILER
-#elif defined(__GNUC__)
+#elif defined(__GNUC__) && (defined(__amd64__) || defined(__i386__))
 #   define USING_GCC_COMPILER
 #   include <cpuid.h>
 #elif defined(_MSC_VER)
@@ -52,8 +52,7 @@ class ProcessorSupport { (public)
 #elif defined(USING_GCC_COMPILER)
         __get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
 #else
-        std::cerr << "ERROR: please define __cpuid() for this build.\n"; 
-        assert(0);
+	return false;
 #endif
         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
     }