From nobody Tue Dec 14 01:43:45 2021 X-Original-To: dev-commits-ports-main@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 5183F18DF8EC; Tue, 14 Dec 2021 01:43:46 +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 4JCh420FMxz3GZD; Tue, 14 Dec 2021 01:43:46 +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 DDA5E1F4DC; Tue, 14 Dec 2021 01:43:45 +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 1BE1hjsq092265; Tue, 14 Dec 2021 01:43:45 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 1BE1hje5092264; Tue, 14 Dec 2021 01:43:45 GMT (envelope-from git) Date: Tue, 14 Dec 2021 01:43:45 GMT Message-Id: <202112140143.1BE1hje5092264@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: eb67c2b94c0b - main - biology/bowtie: Update to 1.3.1 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@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: eb67c2b94c0b5846d825da791060e0b4c72fc248 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1639446226; 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=jZPTIHW2DEsmelqb5lC2oSnoQmpnUd4cI3Abga24+iU=; b=iFIym2sAy23vxk7c6+5flslgkPYfETajygyOfkj3CjULBQxCPpRXZeTsTvMKO/bQJ9iE4C /aNW7AKylw5yBPgnCtOWn9MojKoU0//2WR+c1tGLhA3ae2kHGjDQeI+40zcVtTSo3KNqjV PWOZ8SCQnrDrFRX5WTG9IbAKDoFq3MqtMUalhCSovo+ueiif50wss9C9gjB4LB2lopbfg8 1b52V6Ej3zVSbFuQFiDDwi4reNyF6eOppHnQ/r8//K9IglorWWOkpUjkoHn6of+RkpQVbg 1le4CEruokFuFztnuLkr7uolmVTH7Ha9GWrSjudMfcd1aZOdXXgqaObirWlRbg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1639446226; a=rsa-sha256; cv=none; b=QgMopv1Kc/38l76ztiXfJJGY9iN6VaDqlyOZZP30wAUxAycAotfn4Ox7yBmN22D9CvzuIP YQos9mAjIxilBtauxLUpQE3qb1XLWKbh0xdwBp26rt84GJXnLD8ZD0K0jKU4I/J7qDP8i5 QMT5rLgyKhvq5DRWh44IVvbVf3ufJP3vfSU5ThNZh30FIDqQNOzHRFJ8oVRvNk/HEhmf4K onqFBuLRpVwKJ/c0hpk1j1R4vN1g7czEdU4qRo2d9VaDMldYV4trpf+EoXhDlFv4LqkVxC SfXKR9qD5Jin9B2CdxnCX59ksgZpymc8KfTUneuVjNc063A87J/4yMJDZaHx5w== 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=eb67c2b94c0b5846d825da791060e0b4c72fc248 commit eb67c2b94c0b5846d825da791060e0b4c72fc248 Author: Jason W. Bacon AuthorDate: 2021-12-14 01:41:19 +0000 Commit: Jason W. Bacon CommitDate: 2021-12-14 01:43:44 +0000 biology/bowtie: Update to 1.3.1 Also adds support for aarch64 and powerpc64* Changes: https://github.com/BenLangmead/bowtie/tags PR: 260389 Reported by: pkubaj --- biology/bowtie/Makefile | 22 +++++---- biology/bowtie/distinfo | 5 ++- biology/bowtie/files/patch-Makefile | 60 ++++++------------------- biology/bowtie/files/patch-ebwt.h | 11 ----- biology/bowtie/files/patch-processor__support.h | 11 ----- biology/bowtie/pkg-plist | 5 ++- 6 files changed, 34 insertions(+), 80 deletions(-) diff --git a/biology/bowtie/Makefile b/biology/bowtie/Makefile index 5fb9ffdff3f0..10607fd8a77f 100644 --- a/biology/bowtie/Makefile +++ b/biology/bowtie/Makefile @@ -1,7 +1,6 @@ PORTNAME= bowtie DISTVERSIONPREFIX= v -DISTVERSION= 1.1.2 -PORTREVISION= 9 +DISTVERSION= 1.3.1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -9,21 +8,26 @@ COMMENT= Ultrafast, memory-efficient short read aligner LICENSE= ART10 -# May also work on other 64-bit platforms, but untested -ONLY_FOR_ARCHS= amd64 +ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le -# FIXME: bowtie-align intermittently dumps core when compiled with clang -# GCC 4.2 does not provide good performance -USES= gmake perl5 python:run shebangfix -USE_GCC= yes +# c++11-lib is just for GCC 4.2-based systems +# Remove it when support officially ends +USES= compiler:c++11-lib gmake perl5 python:run shebangfix USE_PERL5= run USE_GITHUB= yes -SHEBANG_FILES= scripts/*.pl bowtie bowtie-build bowtie-inspect +SHEBANG_FILES= scripts/*.pl bowtie bowtie-build scripts/bowtie-hbb.sh \ + bowtie-inspect GH_ACCOUNT= BenLangmead OPTIONS_DEFINE= DOCS +.include + +.if ${ARCH:Mpowerpc64*} || ${ARCH:Maarch64} +MAKE_ENV= POPCNT_CAPABILITY=0 +.endif + post-install: ${MKDIR} ${STAGEDIR}${DATADIR}/scripts ${INSTALL_SCRIPT} \ diff --git a/biology/bowtie/distinfo b/biology/bowtie/distinfo index ffacca889d6c..fbb7362c14e3 100644 --- a/biology/bowtie/distinfo +++ b/biology/bowtie/distinfo @@ -1,2 +1,3 @@ -SHA256 (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 717145f12d599e9b3672981f5444fbbdb8e02bfde2a80eba577e28baa4125ba7 -SIZE (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 7831346 +TIMESTAMP = 1639406970 +SHA256 (BenLangmead-bowtie-v1.3.1_GH0.tar.gz) = 147d9fe9652f7c5f351bfc0eb012e06981986fb43bd6bdfe88a95c02eabc6573 +SIZE (BenLangmead-bowtie-v1.3.1_GH0.tar.gz) = 7672741 diff --git a/biology/bowtie/files/patch-Makefile b/biology/bowtie/files/patch-Makefile index 8f3a35cf59f5..dcf2f7089076 100644 --- a/biology/bowtie/files/patch-Makefile +++ b/biology/bowtie/files/patch-Makefile @@ -1,52 +1,20 @@ ---- Makefile.orig 2015-06-23 16:32:51 UTC +--- Makefile.orig 2021-12-13 20:33:26 UTC +++ Makefile -@@ -8,9 +8,13 @@ bindir = $(prefix)/bin - SEQAN_DIR = SeqAn-1.1 - SEQAN_INC = -I $(SEQAN_DIR) - INC = $(SEQAN_INC) -I third_party --CPP = g++ --CXX = $(CPP) --CC = gcc -+ -+# Use ?= to allow environment CPP, CC, CXX to take precedence. This avoids -+# the need to modify the Makefile on different platforms. Package managers -+# such as FreeBSD ports, MacPorts, etc. set these variables automatically. -+CPP ?= g++ -+CXX ?= $(CPP) -+CC ?= gcc - HEADERS = $(wildcard *.h) - BOWTIE_MM = 1 - BOWTIE_SHARED_MEM = 1 -@@ -90,10 +94,10 @@ PREFETCH_LOCALITY = 2 - PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY) - - ifeq (1,$(WITH_TBB)) -- LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy -+ LIBS = ${LDFLAGS} $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy - EXTRA_FLAGS += -DWITH_TBB - else -- LIBS = $(PTHREAD_LIB) -+ LIBS = ${LDFLAGS} $(PTHREAD_LIB) +@@ -146,7 +146,7 @@ ifeq (32,$(BITS)) endif - SEARCH_LIBS = -@@ -123,7 +127,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p - VERSION = $(shell cat VERSION) - - BITS=32 --ifeq (x86_64,$(shell uname -m)) -+ifeq (amd64,$(shell uname -m)) - BITS=64 - endif - # msys will always be 32 bit so look at the cpu arch instead. -@@ -143,8 +147,8 @@ ifeq (32,$(BITS)) - $(error bowtie2 compilation requires a 64-bit platform ) - endif - --DEBUG_FLAGS = -O0 -g3 -m64 --RELEASE_FLAGS = -O3 -m64 -+DEBUG_FLAGS = -O0 -g3 -+RELEASE_FLAGS = -O + DEBUG_FLAGS = -O0 -g3 +-RELEASE_FLAGS = -O3 ++RELEASE_FLAGS = NOASSERT_FLAGS = -DNDEBUG FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE +@@ -225,7 +225,7 @@ DEFS=-fno-strict-aliasing \ + $(MM_DEF) \ + $(SHMEM_DEF) + +-ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS) ++ALL_FLAGS = $(EXTRA_FLAGS) $(CXXFLAGS) + DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\"" + RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\"" + diff --git a/biology/bowtie/files/patch-ebwt.h b/biology/bowtie/files/patch-ebwt.h deleted file mode 100644 index 4272bbd8303c..000000000000 --- a/biology/bowtie/files/patch-ebwt.h +++ /dev/null @@ -1,11 +0,0 @@ ---- ebwt.h.orig 2018-11-03 20:51:56 UTC -+++ ebwt.h -@@ -860,7 +860,7 @@ public: - TIndexOffU* ftab() const { return _ftab; } - TIndexOffU* eftab() const { return _eftab; } - TIndexOffU* offs() const { return _offs; } -- uint32_t* isa() const { return _isa; } /* check */ -+ uint32_t* isa() const { return (uint32_t)_isa; } /* check */ - TIndexOffU* plen() const { return _plen; } - TIndexOffU* rstarts() const { return _rstarts; } - uint8_t* ebwt() const { return _ebwt; } diff --git a/biology/bowtie/files/patch-processor__support.h b/biology/bowtie/files/patch-processor__support.h deleted file mode 100644 index bbfecedb7a3b..000000000000 --- a/biology/bowtie/files/patch-processor__support.h +++ /dev/null @@ -1,11 +0,0 @@ ---- processor_support.h.orig 2020-07-04 10:42:26 UTC -+++ processor_support.h -@@ -49,7 +49,7 @@ 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”; -+ std::cerr << "ERROR: please define __cpuid() for this build.\n"; - assert(0); - #endif - if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; diff --git a/biology/bowtie/pkg-plist b/biology/bowtie/pkg-plist index e0e8c2056459..0f6efe21b18c 100644 --- a/biology/bowtie/pkg-plist +++ b/biology/bowtie/pkg-plist @@ -26,7 +26,9 @@ bin/bowtie-inspect-s %%DATADIR%%/reads/e_coli_1000_1.fq %%DATADIR%%/reads/e_coli_1000_2.fa %%DATADIR%%/reads/e_coli_1000_2.fq +%%DATADIR%%/reads/e_coli_1000_interleaved.fq %%DATADIR%%/scripts/best_verify.pl +%%DATADIR%%/scripts/bowtie-hbb.sh %%DATADIR%%/scripts/bs_mapability.pl %%DATADIR%%/scripts/build_test.sh %%DATADIR%%/scripts/colorize_fasta.pl @@ -58,6 +60,7 @@ bin/bowtie-inspect-s %%DATADIR%%/scripts/pe_verify.pl %%DATADIR%%/scripts/reconcile_alignments.pl %%DATADIR%%/scripts/reconcile_alignments_pe.pl +%%DATADIR%%/scripts/run-hbb.sh %%PORTDOCS%%%%DOCSDIR%%/README %%PORTDOCS%%%%DOCSDIR%%/manual.html %%PORTDOCS%%%%DOCSDIR%%/release.txt @@ -81,7 +84,7 @@ bin/bowtie-inspect-s %%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi %%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml %%PORTDOCS%%%%DOCSDIR%%/website/other_tools.ssi -%%PORTDOCS%%%%DOCSDIR%%/website/push_langmead.sh +%%PORTDOCS%%%%DOCSDIR%%/website/push.sh %%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi %%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi %%PORTDOCS%%%%DOCSDIR%%/website/top.ssi