mirror of
https://git.FreeBSD.org/ports.git
synced 2024-11-19 00:13:33 +00:00
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 @@
|
||||
PORTNAME= hisat2
|
||||
DISTVERSION= 2.1.0-23
|
||||
DISTVERSIONSUFFIX= -g20f333e
|
||||
DISTVERSIONPREFIX= v
|
||||
DISTVERSION= 2.2.1
|
||||
CATEGORIES= biology perl5 python
|
||||
|
||||
MAINTAINER= jwb@FreeBSD.org
|
||||
@ -9,20 +9,18 @@ COMMENT= Alignment program for mapping next-generation sequencing reads
|
||||
LICENSE= GPLv3
|
||||
LICENSE_FILE= ${WRKSRC}/LICENSE
|
||||
|
||||
# May work on other 64-bit archs, untested
|
||||
ONLY_FOR_ARCHS= amd64
|
||||
ONLY_FOR_ARCHS_REASON= 64-bit code, some assembly language
|
||||
|
||||
USES= gmake perl5 python shebangfix
|
||||
USE_GITHUB= yes
|
||||
|
||||
SHEBANG_FILES= hisat2 hisat2-build hisat2-inspect *.py \
|
||||
scripts/*.sh scripts/*.pl \
|
||||
hisatgenotype_modules/*.py \
|
||||
hisatgenotype_scripts/*.py \
|
||||
hisatgenotype_scripts/*.sh
|
||||
GH_ACCOUNT= infphilo
|
||||
SHEBANG_FILES= hisat2 hisat2-build hisat2-inspect \
|
||||
*.py */*.py */*/*.py */*/*/*.py \
|
||||
scripts/*.sh evaluation/tests/HLA_novel/scripts/*.sh \
|
||||
scripts/*.pl docs_jhu/*.pl
|
||||
GH_ACCOUNT= DaehwanKimLab
|
||||
|
||||
MAKEFILE= ${FILESDIR}/Makefile.pkg
|
||||
CFLAGS+= -Wno-deprecated-declarations -Wno-char-subscripts
|
||||
|
||||
.include <bsd.port.mk>
|
||||
|
||||
@ -1,3 +1,3 @@
|
||||
TIMESTAMP = 1547001889
|
||||
SHA256 (infphilo-hisat2-2.1.0-23-g20f333e_GH0.tar.gz) = 7327fa50f51cd1a0fefe1a379cfeb2f06eefdbbe8f49b04b0d79332080f6be57
|
||||
SIZE (infphilo-hisat2-2.1.0-23-g20f333e_GH0.tar.gz) = 3972398
|
||||
TIMESTAMP = 1637941870
|
||||
SHA256 (DaehwanKimLab-hisat2-v2.2.1_GH0.tar.gz) = f3f4f867d0a6b1f880d64efc19deaa5788c62050e0a4d614ce98b3492f702599
|
||||
SIZE (DaehwanKimLab-hisat2-v2.2.1_GH0.tar.gz) = 6761242
|
||||
|
||||
@ -1,446 +0,0 @@
|
||||
#
|
||||
# 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,$(BOWTIE_SHARED_MEM))
|
||||
SHMEM_DEF = -DBOWTIE_SHARED_MEM
|
||||
endif
|
||||
|
||||
PTHREAD_PKG =
|
||||
PTHREAD_LIB = -lpthread
|
||||
|
||||
SEARCH_LIBS =
|
||||
BUILD_LIBS =
|
||||
INSPECT_LIBS =
|
||||
|
||||
USE_SRA = 0
|
||||
SRA_DEF =
|
||||
SRA_LIB =
|
||||
SERACH_INC =
|
||||
ifeq (1,$(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 = $(PTHREAD_LIB)
|
||||
|
||||
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/
|
||||
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