biology/hisat2: Update to 2.2.1
Changes: https://github.com/DaehwanKimLab/hisat2/tags
This commit is contained in:
Jason W. Bacon
parent
948157a880
commit
d8bc1eb796
@ -1,6 +1,6 @@
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PORTNAME= hisat2
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DISTVERSION= 2.1.0-23
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DISTVERSIONSUFFIX= -g20f333e
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DISTVERSIONPREFIX= v
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DISTVERSION= 2.2.1
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CATEGORIES= biology perl5 python
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MAINTAINER= jwb@FreeBSD.org
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@ -9,20 +9,18 @@ COMMENT= Alignment program for mapping next-generation sequencing reads
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LICENSE= GPLv3
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LICENSE_FILE= ${WRKSRC}/LICENSE
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# May work on other 64-bit archs, untested
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ONLY_FOR_ARCHS= amd64
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ONLY_FOR_ARCHS_REASON= 64-bit code, some assembly language
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USES= gmake perl5 python shebangfix
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USE_GITHUB= yes
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SHEBANG_FILES= hisat2 hisat2-build hisat2-inspect *.py \
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scripts/*.sh scripts/*.pl \
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hisatgenotype_modules/*.py \
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hisatgenotype_scripts/*.py \
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hisatgenotype_scripts/*.sh
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GH_ACCOUNT= infphilo
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SHEBANG_FILES= hisat2 hisat2-build hisat2-inspect \
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*.py */*.py */*/*.py */*/*/*.py \
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scripts/*.sh evaluation/tests/HLA_novel/scripts/*.sh \
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scripts/*.pl docs_jhu/*.pl
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GH_ACCOUNT= DaehwanKimLab
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MAKEFILE= ${FILESDIR}/Makefile.pkg
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CFLAGS+= -Wno-deprecated-declarations -Wno-char-subscripts
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.include <bsd.port.mk>
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@ -1,3 +1,3 @@
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TIMESTAMP = 1547001889
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SHA256 (infphilo-hisat2-2.1.0-23-g20f333e_GH0.tar.gz) = 7327fa50f51cd1a0fefe1a379cfeb2f06eefdbbe8f49b04b0d79332080f6be57
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SIZE (infphilo-hisat2-2.1.0-23-g20f333e_GH0.tar.gz) = 3972398
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TIMESTAMP = 1637941870
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SHA256 (DaehwanKimLab-hisat2-v2.2.1_GH0.tar.gz) = f3f4f867d0a6b1f880d64efc19deaa5788c62050e0a4d614ce98b3492f702599
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SIZE (DaehwanKimLab-hisat2-v2.2.1_GH0.tar.gz) = 6761242
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@ -1,446 +0,0 @@
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#
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# Generic Makefile for package managers
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# J Bacon <bacon4000@gmail.com>
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#
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# This Makefile respects standard make variables provided by package
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# managers, such as CXX, CXXFLAGS, etc. It is intended to work on
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# any POSIX platform. Default behaviour should be similar to the
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# original Makefile.
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#
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# This file is part of HISAT2.
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#
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# HISAT 2 is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# HISAT 2 is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with HISAT. If not, see <http://www.gnu.org/licenses/>.
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#
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INC =
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GCC_PREFIX = $(shell dirname `which gcc`)
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GCC_SUFFIX =
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CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
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CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
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CXX ?= $(CPP)
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CXXFLAGS ?= -O2 -Wall
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INSTALL ?= install
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HEADERS = $(wildcard *.h)
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BOWTIE_MM = 1
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BOWTIE_SHARED_MEM = 0
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MACOS = 0
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ifneq (,$(findstring Darwin,$(shell uname)))
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MACOS = 1
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endif
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# EXTRA_FLAGS += -DPOPCNT_CAPABILITY
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INC += -I third_party
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MM_DEF =
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ifeq (1,$(BOWTIE_MM))
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MM_DEF = -DBOWTIE_MM
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endif
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SHMEM_DEF =
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ifeq (1,$(BOWTIE_SHARED_MEM))
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SHMEM_DEF = -DBOWTIE_SHARED_MEM
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endif
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PTHREAD_PKG =
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PTHREAD_LIB = -lpthread
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SEARCH_LIBS =
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BUILD_LIBS =
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INSPECT_LIBS =
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USE_SRA = 0
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SRA_DEF =
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SRA_LIB =
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SERACH_INC =
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ifeq (1,$(USE_SRA))
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SRA_DEF = -DUSE_SRA
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SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -ldl
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SEARCH_INC += -I$(NCBI_NGS_DIR)/include -I$(NCBI_VDB_DIR)/include
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SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib64 -L$(NCBI_VDB_DIR)/lib64
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endif
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LIBS = $(PTHREAD_LIB)
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SHARED_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
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edit.cpp gfm.cpp \
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reference.cpp ds.cpp multikey_qsort.cpp limit.cpp \
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random_source.cpp tinythread.cpp
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SEARCH_CPPS = qual.cpp pat.cpp \
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read_qseq.cpp aligner_seed_policy.cpp \
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aligner_seed.cpp \
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aligner_seed2.cpp \
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aligner_sw.cpp \
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aligner_sw_driver.cpp aligner_cache.cpp \
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aligner_result.cpp ref_coord.cpp mask.cpp \
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pe.cpp aln_sink.cpp dp_framer.cpp \
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scoring.cpp presets.cpp unique.cpp \
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simple_func.cpp \
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random_util.cpp \
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aligner_bt.cpp sse_util.cpp \
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aligner_swsse.cpp outq.cpp \
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aligner_swsse_loc_i16.cpp \
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aligner_swsse_ee_i16.cpp \
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aligner_swsse_loc_u8.cpp \
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aligner_swsse_ee_u8.cpp \
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aligner_driver.cpp \
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splice_site.cpp
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SEARCH_OBJS = qual.o pat.o \
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read_qseq.o aligner_seed_policy.o \
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aligner_seed.o \
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aligner_seed2.o \
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aligner_sw.o \
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aligner_sw_driver.o aligner_cache.o \
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aligner_result.o ref_coord.o mask.o \
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pe.o aln_sink.o dp_framer.o \
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scoring.o presets.o unique.o \
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simple_func.o \
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random_util.o \
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aligner_bt.o sse_util.o \
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aligner_swsse.o outq.o \
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aligner_swsse_loc_i16.o \
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aligner_swsse_ee_i16.o \
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aligner_swsse_loc_u8.o \
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aligner_swsse_ee_u8.o \
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aligner_driver.o \
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splice_site.o
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BUILD_CPPS = diff_sample.cpp
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HISAT2_CPPS_MAIN = $(SEARCH_CPPS) hisat2_main.cpp
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HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) hisat2_build_main.cpp
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SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
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VERSION = $(shell cat VERSION)
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DEBUG_FLAGS = $(CXXFLAGS) -O0 -g3
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DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
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RELEASE_FLAGS = $(CXXFLAGS)
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RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
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NOASSERT_FLAGS = -DNDEBUG
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FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
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ifeq (1,$(USE_SRA))
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ifeq (1, $(MACOS))
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DEBUG_FLAGS += -mmacosx-version-min=10.6
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RELEASE_FLAGS += -mmacosx-version-min=10.6
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endif
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endif
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HISAT2_BIN_LIST = hisat2-build-s \
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hisat2-build-l \
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hisat2-align-s \
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hisat2-align-l \
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hisat2-inspect-s \
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hisat2-inspect-l
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HISAT2_BIN_LIST_AUX = hisat2-build-s-debug \
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hisat2-build-l-debug \
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hisat2-align-s-debug \
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hisat2-align-l-debug \
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hisat2-inspect-s-debug \
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hisat2-inspect-l-debug
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GENERAL_LIST = $(wildcard scripts/*.sh) \
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$(wildcard scripts/*.pl) \
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$(wildcard *.py) \
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$(wildcard hisatgenotype_modules/*.py) \
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$(wildcard hisatgenotype_scripts/*.py) \
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doc/manual.inc.html \
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doc/README \
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doc/style.css \
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$(wildcard example/index/*.ht2) \
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$(wildcard example/reads/*.fa) \
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example/reference/22_20-21M.fa \
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example/reference/22_20-21M.snp \
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$(PTHREAD_PKG) \
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hisat2 \
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hisat2-build \
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hisat2-inspect \
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AUTHORS \
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LICENSE \
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NEWS \
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MANUAL \
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MANUAL.markdown \
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TUTORIAL \
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VERSION
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ifeq (1,$(WINDOWS))
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HISAT2_BIN_LIST := $(HISAT2_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat
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endif
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# This is helpful on Windows under MinGW/MSYS, where Make might go for
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# the Windows FIND tool instead.
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FIND=$(shell which find)
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SRC_PKG_LIST = $(wildcard *.h) \
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$(wildcard *.hh) \
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$(wildcard *.c) \
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$(wildcard *.cpp) \
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doc/strip_markdown.pl \
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Makefile \
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$(GENERAL_LIST)
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BIN_PKG_LIST = $(GENERAL_LIST)
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.PHONY: all allall both both-debug install
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all: $(HISAT2_BIN_LIST)
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allall: $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)
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both: hisat2-align-s hisat2-align-l hisat2-build-s hisat2-build-l
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both-debug: hisat2-align-s-debug hisat2-align-l-debug hisat2-build-s-debug hisat2-build-l-debug
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DEFS=-fno-strict-aliasing \
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-DHISAT2_VERSION="\"`cat VERSION`\"" \
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-DBUILD_HOST="\"`hostname`\"" \
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-DBUILD_TIME="\"`date`\"" \
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-DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
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$(FILE_FLAGS) \
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$(PREF_DEF) \
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$(MM_DEF) \
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$(SHMEM_DEF)
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#
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# hisat-bp targets
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#
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hisat-bp-bin: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
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$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) \
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$(INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
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$(LIBS) $(SEARCH_LIBS)
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hisat-bp-bin-debug: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
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$(CXX) $(DEBUG_FLAGS) \
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$(DEBUG_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) -DBOWTIE2 \
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$(INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
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$(LIBS) $(SEARCH_LIBS)
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#
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# hisat2-build targets
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#
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hisat2-build-s: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
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$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -DMASSIVE_DATA_RLCSA \
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$(INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
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$(LIBS) $(BUILD_LIBS)
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hisat2-build-l: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
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$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) \
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$(INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
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$(LIBS) $(BUILD_LIBS)
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hisat2-build-s-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
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$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) -DBOWTIE2 -DMASSIVE_DATA_RLCSA \
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$(INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
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$(LIBS) $(BUILD_LIBS)
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hisat2-build-l-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
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$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX \
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$(INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
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$(LIBS) $(BUILD_LIBS)
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#
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# hisat2 targets
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#
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hisat2-align-s: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
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$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) $(SRA_DEF) -DBOWTIE2 $(NOASSERT_FLAGS) \
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$(INC) $(SEARCH_INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
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$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
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hisat2-align-l: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
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$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) $(SRA_DEF) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) \
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$(INC) $(SEARCH_INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
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$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
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|
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hisat2-align-s-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
|
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$(CXX) $(DEBUG_FLAGS) \
|
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$(DEBUG_DEFS) $(EXTRA_FLAGS) \
|
||||
$(DEFS) $(SRA_DEF) -DBOWTIE2 \
|
||||
$(INC) $(SEARCH_INC) \
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-o $@ $< \
|
||||
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
|
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$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
|
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|
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hisat2-align-l-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
|
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$(CXX) $(DEBUG_FLAGS) \
|
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$(DEBUG_DEFS) $(EXTRA_FLAGS) \
|
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$(DEFS) $(SRA_DEF) -DBOWTIE2 -DBOWTIE_64BIT_INDEX \
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$(INC) $(SEARCH_INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
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$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
|
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#
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# hisat2-inspect targets
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#
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hisat2-inspect-s: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
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$(CXX) $(RELEASE_FLAGS) \
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$(RELEASE_DEFS) $(EXTRA_FLAGS) \
|
||||
$(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN \
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$(INC) -I . \
|
||||
-o $@ $< \
|
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$(SHARED_CPPS) \
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$(LIBS) $(INSPECT_LIBS)
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|
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hisat2-inspect-l: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
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$(CXX) $(RELEASE_FLAGS) \
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$(RELEASE_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN \
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$(INC) -I . \
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-o $@ $< \
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$(SHARED_CPPS) \
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$(LIBS) $(INSPECT_LIBS)
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|
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hisat2-inspect-s-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
|
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$(CXX) $(DEBUG_FLAGS) \
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$(DEBUG_DEFS) $(EXTRA_FLAGS) \
|
||||
$(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN \
|
||||
$(INC) -I . \
|
||||
-o $@ $< \
|
||||
$(SHARED_CPPS) \
|
||||
$(LIBS) $(INSPECT_LIBS)
|
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|
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hisat2-inspect-l-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
|
||||
$(CXX) $(DEBUG_FLAGS) \
|
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$(DEBUG_DEFS) $(EXTRA_FLAGS) \
|
||||
$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN \
|
||||
$(INC) -I . \
|
||||
-o $@ $< \
|
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$(SHARED_CPPS) \
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||||
$(LIBS) $(INSPECT_LIBS)
|
||||
|
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%.o: %.cpp
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$(CXX) -c $(RELEASE_FLAGS) \
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||||
$(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
|
||||
|
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hisat2-build.bat:
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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/
|
||||
71
biology/hisat2/files/patch-Makefile
Normal file
71
biology/hisat2/files/patch-Makefile
Normal file
@ -0,0 +1,71 @@
|
||||
--- Makefile.orig 2020-07-24 20:07:54 UTC
|
||||
+++ 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
|
||||
@@ -152,31 +154,9 @@ HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS)
|
||||
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
|
||||
-
|
||||
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
|
||||
@@ -553,6 +533,20 @@ 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:
|
||||
11
biology/hisat2/files/patch-util.h
Normal file
11
biology/hisat2/files/patch-util.h
Normal file
@ -0,0 +1,11 @@
|
||||
--- util.h.orig 2021-11-26 15:40:17 UTC
|
||||
+++ util.h
|
||||
@@ -43,7 +43,7 @@ char* itoa10(const T& value, char* result) {
|
||||
// Only apply negative sign for base 10
|
||||
if(std::numeric_limits<T>::is_signed) {
|
||||
// Avoid compiler warning in cases where T is unsigned
|
||||
- if (value <= 0 && value != 0) *out++ = '-';
|
||||
+ if (value <= 0) *out++ = '-';
|
||||
}
|
||||
reverse( result, out );
|
||||
*out = 0; // terminator
|
||||
@ -7,9 +7,8 @@ bin/hisat2-build-s
|
||||
bin/hisat2-inspect
|
||||
bin/hisat2-inspect-l
|
||||
bin/hisat2-inspect-s
|
||||
libexec/hisat2/compare_HLA_Omixon.py
|
||||
bin/hisat2-repeat
|
||||
libexec/hisat2/convert_quals.pl
|
||||
libexec/hisat2/extract_Omixon_HLA.py
|
||||
libexec/hisat2/extract_exons.py
|
||||
libexec/hisat2/extract_splice_sites.py
|
||||
libexec/hisat2/gen_2b_occ_lookup.pl
|
||||
@ -19,21 +18,8 @@ libexec/hisat2/hisat2_extract_exons.py
|
||||
libexec/hisat2/hisat2_extract_snps_haplotypes_UCSC.py
|
||||
libexec/hisat2/hisat2_extract_snps_haplotypes_VCF.py
|
||||
libexec/hisat2/hisat2_extract_splice_sites.py
|
||||
libexec/hisat2/hisat2_read_statistics.py
|
||||
libexec/hisat2/hisat2_simulate_reads.py
|
||||
libexec/hisat2/hisatgenotype.py
|
||||
libexec/hisat2/hisatgenotype_HLA_genotyping_PGs.py
|
||||
libexec/hisat2/hisatgenotype_assembly_graph.py
|
||||
libexec/hisat2/hisatgenotype_build_genome.py
|
||||
libexec/hisat2/hisatgenotype_convert_codis.py
|
||||
libexec/hisat2/hisatgenotype_extract_codis_data.py
|
||||
libexec/hisat2/hisatgenotype_extract_cyp_data.py
|
||||
libexec/hisat2/hisatgenotype_extract_reads.py
|
||||
libexec/hisat2/hisatgenotype_extract_vars.py
|
||||
libexec/hisat2/hisatgenotype_gene_typing.py
|
||||
libexec/hisat2/hisatgenotype_hla_cyp.py
|
||||
libexec/hisat2/hisatgenotype_locus.py
|
||||
libexec/hisat2/hisatgenotype_locus_samples.py
|
||||
libexec/hisat2/hisatgenotype_typing_common.py
|
||||
libexec/hisat2/infer_fraglen.pl
|
||||
libexec/hisat2/make_a_thaliana_tair.sh
|
||||
libexec/hisat2/make_b_taurus_UMD3.sh
|
||||
@ -49,7 +35,9 @@ libexec/hisat2/make_grch37_snp_tran.sh
|
||||
libexec/hisat2/make_grch37_snp_tran_ercc.sh
|
||||
libexec/hisat2/make_grch37_tran.sh
|
||||
libexec/hisat2/make_grch38.sh
|
||||
libexec/hisat2/make_grch38_rep.sh
|
||||
libexec/hisat2/make_grch38_snp.sh
|
||||
libexec/hisat2/make_grch38_snp_rep.sh
|
||||
libexec/hisat2/make_grch38_snp_tran.sh
|
||||
libexec/hisat2/make_grch38_snp_tran_ercc.sh
|
||||
libexec/hisat2/make_grch38_tran.sh
|
||||
@ -74,8 +62,5 @@ libexec/hisat2/make_sc3.sh
|
||||
libexec/hisat2/make_wbcel235.sh
|
||||
libexec/hisat2/make_wbcel235_tran.sh
|
||||
libexec/hisat2/make_zm3_snp_tran_ercc.sh
|
||||
libexec/hisat2/run_extract_CP.sh
|
||||
libexec/hisat2/run_extract_ILMN.sh
|
||||
libexec/hisat2/run_genotype_build.sh
|
||||
libexec/hisat2/run_hisat2_build.sh
|
||||
libexec/hisat2/run_type_CP.sh
|
||||
libexec/hisat2/sa.py
|
||||
libexec/hisat2/validate_repeat.py
|
||||
|
||||
Loading…
Reference in New Issue
Block a user