head	1.2;
access;
symbols
	pkgsrc-2021Q4:1.1.0.24
	pkgsrc-2021Q4-base:1.1
	pkgsrc-2021Q3:1.1.0.22
	pkgsrc-2021Q3-base:1.1
	pkgsrc-2021Q2:1.1.0.20
	pkgsrc-2021Q2-base:1.1
	pkgsrc-2021Q1:1.1.0.18
	pkgsrc-2021Q1-base:1.1
	pkgsrc-2020Q4:1.1.0.16
	pkgsrc-2020Q4-base:1.1
	pkgsrc-2020Q3:1.1.0.14
	pkgsrc-2020Q3-base:1.1
	pkgsrc-2020Q2:1.1.0.12
	pkgsrc-2020Q2-base:1.1
	pkgsrc-2020Q1:1.1.0.8
	pkgsrc-2020Q1-base:1.1
	pkgsrc-2019Q4:1.1.0.10
	pkgsrc-2019Q4-base:1.1
	pkgsrc-2019Q3:1.1.0.6
	pkgsrc-2019Q3-base:1.1
	pkgsrc-2019Q2:1.1.0.4
	pkgsrc-2019Q2-base:1.1
	pkgsrc-2019Q1:1.1.0.2
	pkgsrc-2019Q1-base:1.1;
locks; strict;
comment	@# @;


1.2
date	2022.03.17.16.01.12;	author bacon;	state dead;
branches;
next	1.1;
commitid	Q8UklxdSfTDWnAwD;

1.1
date	2019.01.15.01.26.29;	author bacon;	state Exp;
branches;
next	;
commitid	BDBV5XMtN1wQKO7B;


desc
@@


1.2
log
@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
@
text
@#
# Generic Makefile for package managers
# J Bacon <bacon4000@@gmail.com>
#
# This Makefile respects standard make variables provided by package
# managers, such as CXX, CXXFLAGS, etc.  It is intended to work on
# any POSIX platform.  Default behaviour should be similar to the
# original Makefile.
#
# This file is part of HISAT2.
#
# HISAT 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# HISAT 2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with HISAT.  If not, see <http://www.gnu.org/licenses/>.
#

INC =
GCC_PREFIX = $(shell dirname `which gcc`)
GCC_SUFFIX =

CC	?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
CPP	?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
CXX	?= $(CPP)
CXXFLAGS ?= -O2 -Wall
INSTALL	?= install

HEADERS = $(wildcard *.h)
BOWTIE_MM = 1
BOWTIE_SHARED_MEM = 0

MACOS = 0
ifneq (,$(findstring Darwin,$(shell uname)))
	MACOS = 1
endif

# EXTRA_FLAGS += -DPOPCNT_CAPABILITY
INC += -I third_party

MM_DEF = 

ifeq (1,$(BOWTIE_MM))
	MM_DEF = -DBOWTIE_MM
endif

SHMEM_DEF = 

ifeq (1,$(BOWTIE_SHARED_MEM))
	SHMEM_DEF = -DBOWTIE_SHARED_MEM
endif

SEARCH_LIBS = 
BUILD_LIBS = 
INSPECT_LIBS =

USE_SRA = 0
SRA_DEF =
SRA_LIB =
SERACH_INC = 
ifeq (1,$(USE_SRA))
	SRA_DEF = -DUSE_SRA
	SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -ldl
	SEARCH_INC += -I$(NCBI_NGS_DIR)/include -I$(NCBI_VDB_DIR)/include
	SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib64 -L$(NCBI_VDB_DIR)/lib64
endif

LIBS = $(LDFLAGS)

SHARED_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
	edit.cpp gfm.cpp \
	reference.cpp ds.cpp multikey_qsort.cpp limit.cpp \
	random_source.cpp tinythread.cpp
SEARCH_CPPS = qual.cpp pat.cpp \
	read_qseq.cpp aligner_seed_policy.cpp \
	aligner_seed.cpp \
	aligner_seed2.cpp \
	aligner_sw.cpp \
	aligner_sw_driver.cpp aligner_cache.cpp \
	aligner_result.cpp ref_coord.cpp mask.cpp \
	pe.cpp aln_sink.cpp dp_framer.cpp \
	scoring.cpp presets.cpp unique.cpp \
	simple_func.cpp \
	random_util.cpp \
	aligner_bt.cpp sse_util.cpp \
	aligner_swsse.cpp outq.cpp \
	aligner_swsse_loc_i16.cpp \
	aligner_swsse_ee_i16.cpp \
	aligner_swsse_loc_u8.cpp \
	aligner_swsse_ee_u8.cpp \
	aligner_driver.cpp \
	splice_site.cpp 

SEARCH_OBJS = qual.o pat.o \
	read_qseq.o aligner_seed_policy.o \
	aligner_seed.o \
	aligner_seed2.o \
	aligner_sw.o \
	aligner_sw_driver.o aligner_cache.o \
	aligner_result.o ref_coord.o mask.o \
	pe.o aln_sink.o dp_framer.o \
	scoring.o presets.o unique.o \
	simple_func.o \
	random_util.o \
	aligner_bt.o sse_util.o \
	aligner_swsse.o outq.o \
	aligner_swsse_loc_i16.o \
	aligner_swsse_ee_i16.o \
	aligner_swsse_loc_u8.o \
	aligner_swsse_ee_u8.o \
	aligner_driver.o \
	splice_site.o 

BUILD_CPPS = diff_sample.cpp

HISAT2_CPPS_MAIN = $(SEARCH_CPPS) hisat2_main.cpp
HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) hisat2_build_main.cpp

SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
VERSION = $(shell cat VERSION)

DEBUG_FLAGS    = $(CXXFLAGS) -O0 -g3
DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
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

ifeq (1,$(USE_SRA))
	ifeq (1, $(MACOS))
		DEBUG_FLAGS += -mmacosx-version-min=10.6
		RELEASE_FLAGS += -mmacosx-version-min=10.6
	endif
endif


HISAT2_BIN_LIST = hisat2-build-s \
	hisat2-build-l \
	hisat2-align-s \
	hisat2-align-l \
	hisat2-inspect-s \
	hisat2-inspect-l
HISAT2_BIN_LIST_AUX = hisat2-build-s-debug \
	hisat2-build-l-debug \
	hisat2-align-s-debug \
	hisat2-align-l-debug \
	hisat2-inspect-s-debug \
	hisat2-inspect-l-debug

GENERAL_LIST = $(wildcard scripts/*.sh) \
	$(wildcard scripts/*.pl) \
	$(wildcard *.py) \
	$(wildcard hisatgenotype_modules/*.py) \
	$(wildcard hisatgenotype_scripts/*.py) \
	doc/manual.inc.html \
	doc/README \
	doc/style.css \
	$(wildcard example/index/*.ht2) \
	$(wildcard example/reads/*.fa) \
	example/reference/22_20-21M.fa \
	example/reference/22_20-21M.snp \
	$(PTHREAD_PKG) \
	hisat2 \
	hisat2-build \
	hisat2-inspect \
	AUTHORS \
	LICENSE \
	NEWS \
	MANUAL \
	MANUAL.markdown \
	TUTORIAL \
	VERSION

ifeq (1,$(WINDOWS))
	HISAT2_BIN_LIST := $(HISAT2_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat 
endif

# This is helpful on Windows under MinGW/MSYS, where Make might go for
# the Windows FIND tool instead.
FIND=$(shell which find)

SRC_PKG_LIST = $(wildcard *.h) \
	$(wildcard *.hh) \
	$(wildcard *.c) \
	$(wildcard *.cpp) \
	doc/strip_markdown.pl \
	Makefile \
	$(GENERAL_LIST)

BIN_PKG_LIST = $(GENERAL_LIST)

.PHONY: all allall both both-debug install

all: $(HISAT2_BIN_LIST)

allall: $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)

both: hisat2-align-s hisat2-align-l hisat2-build-s hisat2-build-l

both-debug: hisat2-align-s-debug hisat2-align-l-debug hisat2-build-s-debug hisat2-build-l-debug

DEFS=-fno-strict-aliasing \
     -DHISAT2_VERSION="\"`cat VERSION`\"" \
     -DBUILD_HOST="\"`hostname`\"" \
     -DBUILD_TIME="\"`date`\"" \
     -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
     $(FILE_FLAGS) \
     $(PREF_DEF) \
     $(MM_DEF) \
     $(SHMEM_DEF)

#
# hisat-bp targets
#

hisat-bp-bin: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) \
	$(INC) \
	-o $@@ $< \
	$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
	$(LIBS) $(SEARCH_LIBS)

hisat-bp-bin-debug: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
	$(CXX) $(DEBUG_FLAGS) \
	$(DEBUG_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) -DBOWTIE2 \
	$(INC) \
	-o $@@ $< \
	$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
	$(LIBS) $(SEARCH_LIBS)


#
# hisat2-build targets
#

hisat2-build-s: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -DMASSIVE_DATA_RLCSA \
	$(INC) \
	-o $@@ $< \
	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
	$(LIBS) $(BUILD_LIBS)

hisat2-build-l: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) \
	$(INC) \
	-o $@@ $< \
	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
	$(LIBS) $(BUILD_LIBS)

hisat2-build-s-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
	$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) -DBOWTIE2 -DMASSIVE_DATA_RLCSA \
	$(INC) \
	-o $@@ $< \
	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
	$(LIBS) $(BUILD_LIBS)

hisat2-build-l-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
	$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX \
	$(INC) \
	-o $@@ $< \
	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
	$(LIBS) $(BUILD_LIBS)

#
# hisat2 targets
#

hisat2-align-s: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) $(SRA_DEF) -DBOWTIE2 $(NOASSERT_FLAGS) \
	$(INC) $(SEARCH_INC) \
	-o $@@ $< \
	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)

hisat2-align-l: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) $(SRA_DEF) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) \
	$(INC) $(SEARCH_INC) \
	-o $@@ $< \
	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)

hisat2-align-s-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
	$(CXX) $(DEBUG_FLAGS) \
	$(DEBUG_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) $(SRA_DEF) -DBOWTIE2 \
	$(INC) $(SEARCH_INC) \
	-o $@@ $< \
	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)

hisat2-align-l-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
	$(CXX) $(DEBUG_FLAGS) \
	$(DEBUG_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) $(SRA_DEF) -DBOWTIE2 -DBOWTIE_64BIT_INDEX \
	$(INC) $(SEARCH_INC) \
	-o $@@ $< \
	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)

#
# hisat2-inspect targets
#

hisat2-inspect-s: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
	$(CXX) $(RELEASE_FLAGS) \
	$(RELEASE_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN \
	$(INC) -I . \
	-o $@@ $< \
	$(SHARED_CPPS) \
	$(LIBS) $(INSPECT_LIBS)

hisat2-inspect-l: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
	$(CXX) $(RELEASE_FLAGS) \
	$(RELEASE_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN \
	$(INC) -I . \
	-o $@@ $< \
	$(SHARED_CPPS) \
	$(LIBS) $(INSPECT_LIBS)

hisat2-inspect-s-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS) 
	$(CXX) $(DEBUG_FLAGS) \
	$(DEBUG_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN \
	$(INC) -I . \
	-o $@@ $< \
	$(SHARED_CPPS) \
	$(LIBS) $(INSPECT_LIBS)

hisat2-inspect-l-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS) 
	$(CXX) $(DEBUG_FLAGS) \
	$(DEBUG_DEFS) $(EXTRA_FLAGS) \
	$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN \
	$(INC) -I . \
	-o $@@ $< \
	$(SHARED_CPPS) \
	$(LIBS) $(INSPECT_LIBS)

%.o: %.cpp
	$(CXX) -c $(RELEASE_FLAGS) \
		$(RELEASE_DEFS) $(EXTRA_FLAGS) \
		$(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN \
		$(INC) -I . $< -o $@@ $<

hisat2: ;

hisat2.bat:
	echo "@@echo off" > hisat2.bat
	echo "perl %~dp0/hisat2 %*" >> hisat2.bat

hisat2-build.bat:
	echo "@@echo off" > hisat2-build.bat
	echo "python %~dp0/hisat2-build %*" >> hisat2-build.bat

hisat2-inspect.bat:
	echo "@@echo off" > hisat2-inspect.bat
	echo "python %~dp0/hisat2-inspect %*" >> hisat2-inspect.bat


.PHONY: hisat2-src
hisat2-src: $(SRC_PKG_LIST)
	chmod a+x scripts/*.sh scripts/*.pl
	mkdir .src.tmp
	mkdir .src.tmp/hisat2-$(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 .
	rm -rf .src.tmp

.PHONY: hisat2-bin
hisat2-bin: $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)
	chmod a+x scripts/*.sh scripts/*.pl
	rm -rf .bin.tmp
	mkdir .bin.tmp
	mkdir .bin.tmp/hisat2-$(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 .
	rm -rf .bin.tmp

.PHONY: doc
doc: doc/manual.inc.html MANUAL

doc/manual.inc.html: MANUAL.markdown
	pandoc -T "HISAT2 Manual" -o $@@ \
	 --from markdown --to HTML --toc $^
	perl -i -ne \
	 '$$w=0 if m|^</body>|;print if $$w;$$w=1 if m|^<body>|;' $@@

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 *.py \
		hisatgenotype_modules/hisat*.py \
		hisatgenotype_scripts/*.py hisatgenotype_scripts/*.sh \
		${DESTDIR}${PREFIX}/libexec/hisat2

.PHONY: clean
clean:
	rm -f $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) \
	$(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) \
	hisat2-src.zip hisat2-bin.zip
	rm -f core.* .tmp.head
	rm -rf *.dSYM

.PHONY: push-doc
push-doc: doc/manual.inc.html
	scp doc/*.*html doc/indexes.txt salz-dmz:/ccb/salz7-data/www/ccb.jhu.edu/html/software/hisat2/
@


1.1
log
@biology/hisat2: import hisat2-2.1.0.23

HISAT2 is a fast and sensitive alignment program for mapping next-generation
sequencing reads (both DNA and RNA) to a population of human genomes (as well
as to a single reference genome).
@
text
@@