git: d8bc1eb7963a - main - biology/hisat2: Update to 2.2.1
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Date: Fri, 26 Nov 2021 22:06:33 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=d8bc1eb7963a6f62b707404af33e0256ac2f6d99
commit d8bc1eb7963a6f62b707404af33e0256ac2f6d99
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2021-11-26 22:03:52 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2021-11-26 22:05:43 +0000
biology/hisat2: Update to 2.2.1
Changes: https://github.com/DaehwanKimLab/hisat2/tags
---
biology/hisat2/Makefile | 18 +-
biology/hisat2/distinfo | 6 +-
biology/hisat2/files/Makefile.pkg | 446 ------------------------------------
biology/hisat2/files/patch-Makefile | 71 ++++++
biology/hisat2/files/patch-util.h | 11 +
biology/hisat2/pkg-plist | 27 +--
6 files changed, 99 insertions(+), 480 deletions(-)
diff --git a/biology/hisat2/Makefile b/biology/hisat2/Makefile
index 0b440ca813c0..ae0ad38fbe7d 100644
--- a/biology/hisat2/Makefile
+++ b/biology/hisat2/Makefile
@@ -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>
diff --git a/biology/hisat2/distinfo b/biology/hisat2/distinfo
index 0807a6365a28..7cfdc88f2291 100644
--- a/biology/hisat2/distinfo
+++ b/biology/hisat2/distinfo
@@ -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
diff --git a/biology/hisat2/files/Makefile.pkg b/biology/hisat2/files/Makefile.pkg
deleted file mode 100644
index 451fd441c793..000000000000
--- a/biology/hisat2/files/Makefile.pkg
+++ /dev/null
@@ -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/
diff --git a/biology/hisat2/files/patch-Makefile b/biology/hisat2/files/patch-Makefile
new file mode 100644
index 000000000000..856bf8d629b6
--- /dev/null
+++ b/biology/hisat2/files/patch-Makefile
@@ -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:
diff --git a/biology/hisat2/files/patch-util.h b/biology/hisat2/files/patch-util.h
new file mode 100644
index 000000000000..43c3aa88400c
--- /dev/null
+++ b/biology/hisat2/files/patch-util.h
@@ -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
diff --git a/biology/hisat2/pkg-plist b/biology/hisat2/pkg-plist
index 8b92bbe4f588..b6d115a7a015 100644
--- a/biology/hisat2/pkg-plist
+++ b/biology/hisat2/pkg-plist
@@ -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