From nobody Fri Nov 26 22:06:33 2021 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id A8A1918A16DF; Fri, 26 Nov 2021 22:06:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4J183F2cWmz4l5d; Fri, 26 Nov 2021 22:06:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 3BB0A10B05; Fri, 26 Nov 2021 22:06:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 1AQM6XB6017522; Fri, 26 Nov 2021 22:06:33 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 1AQM6XCj017521; Fri, 26 Nov 2021 22:06:33 GMT (envelope-from git) Date: Fri, 26 Nov 2021 22:06:33 GMT Message-Id: <202111262206.1AQM6XCj017521@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: d8bc1eb7963a - main - biology/hisat2: Update to 2.2.1 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: d8bc1eb7963a6f62b707404af33e0256ac2f6d99 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1637964393; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=YNMVZes9Ri8QfeVdB9BiAXEXXnUsxnaYE1pPi0Tx5tc=; b=M22bNauiaFMyee139Wn3a+UH7ySSot8ymxmX9d9Ts2ITNuc5IVnewA9nTr6Mf91oFWc1CV eTcD4AAQ9oEQKgnlDHHD8XthWVmsfxFEnAR2ffq1XqKMPPEutudD7UTvCxXSVnn7Kq2AuA SUe/XHzkhnplBtMH4v2TjmwNhox02WKczYgNMRtZR0mf95WRpSwsLXUg6LI4fqZMeXGtq8 IQvaOPFhWg8iVArWQ34BqLYMbFWcRbWQ1yM07Ql+vrrnsZJRN9c+DGMr4r8L4pTZqJXXy7 +Ur0qRXiHWUDE+vIOWO7sGUr7zeaWHeXbtZcT1roplFO0i0k1sJs5DJ+O1SfJw== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1637964393; a=rsa-sha256; cv=none; b=o4PT92B3gjyOrIvCRR9fqxEOgrL7pBm2YQBSUfLSzA5elgSRKGNG5xTZ8mhy3NZ4XGyocu zeCHOHHNsBYUVEJlNz8+APGrWPEYthpuB+aNL7BrNH78BfhCfTtB+DCCQ9CZOAcLbwekJx 1S0b+KT6SYQCjaKZz78TKwE9xTZfvEA2WH+QyScrj97esv8cY+xEz7I358r5yLU1hmuLNN UmD4jA7M1n4boZ1nwEyENFg8O0UqBCbfjUr7Ue/uJZs2/C8WbE+agUh/9l0/saWCJJrsJq rBMWZXjZrQS9WT4s929CkAQGbWV9Y3BBVRiybXL54I/+ecOoT12NsJboQQpk4Q== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=d8bc1eb7963a6f62b707404af33e0256ac2f6d99 commit d8bc1eb7963a6f62b707404af33e0256ac2f6d99 Author: Jason W. Bacon AuthorDate: 2021-11-26 22:03:52 +0000 Commit: Jason W. Bacon 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 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 -# -# 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 . -# - -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 \ - '$$w=0 if m|^|;print if $$w;$$w=1 if m|^|;' $@ - -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::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