Received: from mail.netbsd.org (mail.netbsd.org [199.233.217.200]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) (Client CN "mail.NetBSD.org", Issuer "mail.NetBSD.org CA" (not verified)) by mollari.NetBSD.org (Postfix) with ESMTPS id 2D4611A921F for ; Thu, 17 Mar 2022 16:01:15 +0000 (UTC) Received: by mail.netbsd.org (Postfix, from userid 605) id 7F3EE84EE0; Thu, 17 Mar 2022 16:01:14 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id A83F284EC7 for ; Thu, 17 Mar 2022 16:01:13 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([IPv6:::1]) by localhost (mail.netbsd.org [IPv6:::1]) (amavisd-new, port 10025) with ESMTP id pthEA4eAtLv7 for ; Thu, 17 Mar 2022 16:01:12 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.NetBSD.org [IPv6:2001:470:a085:999:28c:faff:fe03:5984]) by mail.netbsd.org (Postfix) with ESMTP id 6CF2D84EA7 for ; Thu, 17 Mar 2022 16:01:12 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 606D2FB24; Thu, 17 Mar 2022 16:01:12 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_164753287232550" MIME-Version: 1.0 Date: Thu, 17 Mar 2022 16:01:12 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/hisat2 To: pkgsrc-changes@NetBSD.org Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20220317160112.606D2FB24@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_164753287232550 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Thu Mar 17 16:01:12 UTC 2022 Modified Files: pkgsrc/biology/hisat2: Makefile PLIST distinfo pkgsrc/biology/hisat2/patches: patch-hisat2 Added Files: pkgsrc/biology/hisat2/patches: patch-Makefile patch-processor__support.h Removed Files: pkgsrc/biology/hisat2/files: Makefile.pkg Log Message: biology/hisat2: Update to 2.2.1 pkgsrc fix: Unbreak build on Darwin Add python3 support Several bug fixes and enhancements Changes: https://github.com/DaehwanKimLab/hisat2/tags To generate a diff of this commit: cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/hisat2/Makefile cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/hisat2/PLIST cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/hisat2/distinfo cvs rdiff -u -r1.1 -r0 pkgsrc/biology/hisat2/files/Makefile.pkg cvs rdiff -u -r0 -r1.1 pkgsrc/biology/hisat2/patches/patch-Makefile \ pkgsrc/biology/hisat2/patches/patch-processor__support.h cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/hisat2/patches/patch-hisat2 Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_164753287232550 Content-Disposition: inline Content-Length: 12281 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/hisat2/Makefile diff -u pkgsrc/biology/hisat2/Makefile:1.6 pkgsrc/biology/hisat2/Makefile:1.7 --- pkgsrc/biology/hisat2/Makefile:1.6 Mon May 24 19:49:11 2021 +++ pkgsrc/biology/hisat2/Makefile Thu Mar 17 16:01:11 2022 @@ -1,10 +1,9 @@ -# $NetBSD: Makefile,v 1.6 2021/05/24 19:49:11 wiz Exp $ +# $NetBSD: Makefile,v 1.7 2022/03/17 16:01:11 bacon Exp $ -DISTNAME= hisat2-2.1.0.23 -PKGREVISION= 5 +DISTNAME= hisat2-2.2.1 CATEGORIES= biology -MASTER_SITES= ${MASTER_SITE_GITHUB:=infphilo/} -GITHUB_TAG= 20f333e2cfe7ff4d1362b248912893e2644683d7 +MASTER_SITES= ${MASTER_SITE_GITHUB:=DaehwanKimLab/} +GITHUB_TAG= v${PKGVERSION_NOREV} MAINTAINER= bacon@NetBSD.org HOMEPAGE= https://ccb.jhu.edu/software/hisat2/index.shtml @@ -17,13 +16,16 @@ ONLY_FOR_PLATFORM= *-*-x86_64 USE_LANGUAGES= c c++ USE_TOOLS+= bash gmake perl -REPLACE_BASH= hisatgenotype_scripts/*.sh -REPLACE_PERL= hisat2 scripts/*.sh scripts/*.pl -REPLACE_PYTHON= *.py hisat2-build hisat2-inspect -REPLACE_PYTHON+= hisatgenotype_modules/*.py hisatgenotype_scripts/*.py +REPLACE_BASH= scripts/*.sh +REPLACE_PERL= hisat2 scripts/*.sh scripts/*.pl scripts/*.py +REPLACE_PYTHON= *.py scripts/*.py hisat2-build hisat2-inspect -MAKE_FILE= ${FILESDIR}/Makefile.pkg PTHREAD_AUTO_VARS= yes +WRKSRC= ${WRKDIR}/hisat2-2.2.1 + +# Unbreak #include on case-insensitive file systems +post-patch: + ${MV} ${WRKSRC}/VERSION ${WRKSRC}/HISAT2_VERSION .include "../../lang/python/application.mk" .include "../../mk/pthread.buildlink3.mk" Index: pkgsrc/biology/hisat2/PLIST diff -u pkgsrc/biology/hisat2/PLIST:1.1 pkgsrc/biology/hisat2/PLIST:1.2 --- pkgsrc/biology/hisat2/PLIST:1.1 Tue Jan 15 01:26:29 2019 +++ pkgsrc/biology/hisat2/PLIST Thu Mar 17 16:01:11 2022 @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.1 2019/01/15 01:26:29 bacon Exp $ +@comment $NetBSD: PLIST,v 1.2 2022/03/17 16:01:11 bacon Exp $ bin/hisat2 bin/hisat2-align-l bin/hisat2-align-s @@ -8,9 +8,8 @@ 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 @@ -20,21 +19,8 @@ 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 @@ -50,7 +36,9 @@ 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 @@ -75,8 +63,5 @@ 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 Index: pkgsrc/biology/hisat2/distinfo diff -u pkgsrc/biology/hisat2/distinfo:1.3 pkgsrc/biology/hisat2/distinfo:1.4 --- pkgsrc/biology/hisat2/distinfo:1.3 Tue Oct 26 10:03:40 2021 +++ pkgsrc/biology/hisat2/distinfo Thu Mar 17 16:01:11 2022 @@ -1,6 +1,8 @@ -$NetBSD: distinfo,v 1.3 2021/10/26 10:03:40 nia Exp $ +$NetBSD: distinfo,v 1.4 2022/03/17 16:01:11 bacon Exp $ -BLAKE2s (hisat2-2.1.0.23-20f333e2cfe7ff4d1362b248912893e2644683d7.tar.gz) = 6b114a873cfb9fa79a3e5e8d72495893d4d3fbadebc924e5826e5de2176e1397 -SHA512 (hisat2-2.1.0.23-20f333e2cfe7ff4d1362b248912893e2644683d7.tar.gz) = 5514f7462a6738e5fed5ef3bd2eb782e867178cd68eb36324407628b446a151d096326d859b2986877a26206ad182281ecac29f2abd01991c0640c5e4c5e5e0b -Size (hisat2-2.1.0.23-20f333e2cfe7ff4d1362b248912893e2644683d7.tar.gz) = 3975385 bytes -SHA1 (patch-hisat2) = ea55c8a99dcd2fd3651e832fbb402b94d0ea3fed +BLAKE2s (hisat2-2.2.1.tar.gz) = 1cc424a10f1fcf25c70294bef3b21e67b07cebcb7b73e36c0176a2dfdec51bdb +SHA512 (hisat2-2.2.1.tar.gz) = a5a688ad0ccfaf326b3ec6dc97206995306aa6f5b6e58223c2113adbca2745f1e8205b436fdf8e01f42da7a38718f9f3bf214b951fb5360d53247d99a0bdbf46 +Size (hisat2-2.2.1.tar.gz) = 6761242 bytes +SHA1 (patch-Makefile) = 067b766ecebacd840db4a287bba25d2d2264b339 +SHA1 (patch-hisat2) = 6010f5fcc1e7dfcb383a4defc4e3d9f06322370d +SHA1 (patch-processor__support.h) = 56d9cd4ba18e37879acba521a0f431fe2b4290af Index: pkgsrc/biology/hisat2/patches/patch-hisat2 diff -u pkgsrc/biology/hisat2/patches/patch-hisat2:1.1 pkgsrc/biology/hisat2/patches/patch-hisat2:1.2 --- pkgsrc/biology/hisat2/patches/patch-hisat2:1.1 Tue Jan 15 01:26:29 2019 +++ pkgsrc/biology/hisat2/patches/patch-hisat2 Thu Mar 17 16:01:12 2022 @@ -1,6 +1,6 @@ -$NetBSD: patch-hisat2,v 1.1 2019/01/15 01:26:29 bacon Exp $ +$NetBSD: patch-hisat2,v 1.2 2022/03/17 16:01:12 bacon Exp $ -# Limit Windows-specific patches to Windows +# Support BSD, etc. --- hisat2.orig 2018-11-07 21:43:32 UTC +++ hisat2 Added files: Index: pkgsrc/biology/hisat2/patches/patch-Makefile diff -u /dev/null pkgsrc/biology/hisat2/patches/patch-Makefile:1.1 --- /dev/null Thu Mar 17 16:01:12 2022 +++ pkgsrc/biology/hisat2/patches/patch-Makefile Thu Mar 17 16:01:12 2022 @@ -0,0 +1,145 @@ +$NetBSD: patch-Makefile,v 1.1 2022/03/17 16:01:12 bacon Exp $ + +# Respect env + +--- Makefile.orig 2020-07-24 20:07:54.000000000 +0000 ++++ 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 = $(wildcard *.h) + BOWTIE_MM = 1 + BOWTIE_SHARED_MEM = 0 +@@ -55,7 +57,7 @@ ifneq (,$(findstring Darwin,$(shell unam + MACOS = 1 + endif + +-EXTRA_FLAGS += -DPOPCNT_CAPABILITY -std=c++11 ++EXTRA_FLAGS += -std=c++11 + INC += -I. -I third_party + + MM_DEF = +@@ -150,33 +152,11 @@ HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) h + HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS) hisat2_repeat_main.cpp + + 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 ++HISAT2_VERSION = $(shell cat HISAT2_VERSION) + + 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 +@@ -251,7 +231,7 @@ GENERAL_LIST = $(wildcard scripts/*.sh) + MANUAL \ + MANUAL.markdown \ + TUTORIAL \ +- VERSION ++ HISAT2_VERSION + + ifeq (1,$(WINDOWS)) + HISAT2_BIN_LIST := $(HISAT2_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat +@@ -287,7 +267,7 @@ repeat: hisat2-repeat + repeat-debug: hisat2-repeat-debug + + DEFS=-fno-strict-aliasing \ +- -DHISAT2_VERSION="\"`cat VERSION`\"" \ ++ -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" \ + -DBUILD_HOST="\"`hostname`\"" \ + -DBUILD_TIME="\"`date`\"" \ + -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \ +@@ -517,12 +497,12 @@ hisat2-inspect.bat: + hisat2-src: $(SRC_PKG_LIST) + chmod a+x scripts/*.sh scripts/*.pl + mkdir .src.tmp +- mkdir .src.tmp/hisat2-$(VERSION) ++ mkdir .src.tmp/hisat2-$(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 . ++ mv tmp.zip .src.tmp/hisat2-$(HISAT2_VERSION) ++ cd .src.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip ++ cd .src.tmp ; zip -r hisat2-$(HISAT2_VERSION)-source.zip hisat2-$(HISAT2_VERSION) ++ cp .src.tmp/hisat2-$(HISAT2_VERSION)-source.zip . + rm -rf .src.tmp + + .PHONY: hisat2-bin +@@ -530,16 +510,16 @@ hisat2-bin: $(BIN_PKG_LIST) $(HISAT2_BIN + chmod a+x scripts/*.sh scripts/*.pl + rm -rf .bin.tmp + mkdir .bin.tmp +- mkdir .bin.tmp/hisat2-$(VERSION) ++ mkdir .bin.tmp/hisat2-$(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 . ++ mv tmp.zip .bin.tmp/hisat2-$(HISAT2_VERSION) ++ cd .bin.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip ++ cd .bin.tmp ; zip -r hisat2-$(HISAT2_VERSION)-$(BITS).zip hisat2-$(HISAT2_VERSION) ++ cp .bin.tmp/hisat2-$(HISAT2_VERSION)-$(BITS).zip . + rm -rf .bin.tmp + + .PHONY: doc +@@ -554,6 +534,20 @@ 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: + rm -f $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) \ Index: pkgsrc/biology/hisat2/patches/patch-processor__support.h diff -u /dev/null pkgsrc/biology/hisat2/patches/patch-processor__support.h:1.1 --- /dev/null Thu Mar 17 16:01:12 2022 +++ pkgsrc/biology/hisat2/patches/patch-processor__support.h Thu Mar 17 16:01:12 2022 @@ -0,0 +1,25 @@ +$NetBSD: patch-processor__support.h,v 1.1 2022/03/17 16:01:12 bacon Exp $ + +# Support non-x86 + +--- processor_support.h.orig 2020-07-24 20:07:54 UTC ++++ processor_support.h +@@ -12,7 +12,7 @@ + + #if defined(__INTEL_COMPILER) + # define USING_INTEL_COMPILER +-#elif defined(__GNUC__) ++#elif defined(__GNUC__) && (defined(__amd64__) || defined(__i386__)) + # define USING_GCC_COMPILER + # include + #elif defined(_MSC_VER) +@@ -52,8 +52,7 @@ class ProcessorSupport { (public) + #elif defined(USING_GCC_COMPILER) + __get_cpuid(0x1, ®s.EAX, ®s.EBX, ®s.ECX, ®s.EDX); + #else +- std::cerr << "ERROR: please define __cpuid() for this build.\n"; +- assert(0); ++ return false; + #endif + if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; + } --_----------=_164753287232550--