From owner-svn-ports-all@freebsd.org Tue Dec 11 07:43:46 2018 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 501241324BF2; Tue, 11 Dec 2018 07:43:46 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id E851788FA7; Tue, 11 Dec 2018 07:43:45 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id C923F2C885; Tue, 11 Dec 2018 07:43:45 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id wBB7hjfi098115; Tue, 11 Dec 2018 07:43:45 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id wBB7hj3O098112; Tue, 11 Dec 2018 07:43:45 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201812110743.wBB7hj3O098112@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Tue, 11 Dec 2018 07:43:45 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r487222 - head/biology/mummer X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: head/biology/mummer X-SVN-Commit-Revision: 487222 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: E851788FA7 X-Spamd-Result: default: False [-2.96 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.999,0]; NEURAL_HAM_SHORT(-0.96)[-0.964,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US]; NEURAL_HAM_LONG(-1.00)[-0.998,0] X-Rspamd-Server: mx1.freebsd.org X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 11 Dec 2018 07:43:46 -0000 Author: yuri Date: Tue Dec 11 07:43:45 2018 New Revision: 487222 URL: https://svnweb.freebsd.org/changeset/ports/487222 Log: biology/mummer: Update 3.23 -> 4.0.0beta2-2 Port changes: * Moved to github * It now installs itself * It uses yaggo during build Modified: head/biology/mummer/Makefile head/biology/mummer/distinfo head/biology/mummer/pkg-plist Modified: head/biology/mummer/Makefile ============================================================================== --- head/biology/mummer/Makefile Tue Dec 11 07:23:54 2018 (r487221) +++ head/biology/mummer/Makefile Tue Dec 11 07:43:45 2018 (r487222) @@ -2,46 +2,28 @@ # $FreeBSD$ PORTNAME= mummer -PORTVERSION= 3.23 -PORTREVISION= 2 +DISTVERSIONPREFIX= v +DISTVERSION= 4.0.0beta2-2 +DISTVERSIONSUFFIX= -g277dac5 CATEGORIES= biology -MASTER_SITES= SF -DISTNAME= MUMmer${PORTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Modular system for rapid whole genome alignment LICENSE= ART10 -LICENSE_FILE= ${WRKSRC}/LICENSE +LICENSE_FILE= ${WRKSRC}/LICENSE.md -USES= gmake perl5 shebangfix +BUILD_DEPENDS= yaggo:devel/yaggo -SHEBANG_FILES= scripts/*.csh scripts/*.pl -SHEBANG_LANG= csh +USES= autoreconf gmake libtool perl5 shebangfix +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --disable-static +USE_GITHUB= yes +GH_ACCOUNT= ${PORTNAME}4 +USE_LDCONFIG= yes + +SHEBANG_FILES= scripts/*.pl perl_OLD_CMD= __PERL_PATH -csh_OLD_CMD= __CSH_PATH -csh_CMD= /bin/csh _SHEBANG_REINPLACE_ARGS+= -e "s|__BIN_DIR|${PREFIX}/bin|g;s|__AUX_BIN_DIR|${PREFIX}/libexec/mummer|g;s|__SCRIPT_DIR|${PREFIX}/libexec/mummer|g" - -PROGRAMS= annotate combineMUMs delta-filter gaps \ - mgaps mummer repeat-match show-aligns \ - show-coords show-diff show-snps show-tiling -SCRIPTS= dnadiff.pl exact-tandems.csh mapview.pl mummerplot.pl nucmer.pl \ - nucmer2xfig.pl promer.pl run-mummer1.csh run-mummer3.csh -LIBEXEC= Foundation.pm tandem-repeat.awk -DOCUMENTS= COPYRIGHT INSTALL LICENSE README - -OPTIONS_DEFINE= DOCS - -do-install: - ${INSTALL_PROGRAM} ${PROGRAMS:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin -.for file in ${SCRIPTS} - ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${file} ${STAGEDIR}${PREFIX}/bin/${file:R} -.endfor - @${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} - ${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/* ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} - ${INSTALL_DATA} ${LIBEXEC:S|^|${WRKSRC}/scripts/|} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} - @${MKDIR} ${STAGEDIR}${DOCSDIR} - ${INSTALL_DATA} ${DOCUMENTS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} .include Modified: head/biology/mummer/distinfo ============================================================================== --- head/biology/mummer/distinfo Tue Dec 11 07:23:54 2018 (r487221) +++ head/biology/mummer/distinfo Tue Dec 11 07:43:45 2018 (r487222) @@ -1,3 +1,3 @@ -TIMESTAMP = 1509357521 -SHA256 (MUMmer3.23.tar.gz) = 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f -SIZE (MUMmer3.23.tar.gz) = 3160143 +TIMESTAMP = 1544513160 +SHA256 (mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz) = 4b77fb57f0e7994ed0cb9886de23ce620b89cb16734df82ba492dbc750e387f1 +SIZE (mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz) = 18369428 Modified: head/biology/mummer/pkg-plist ============================================================================== --- head/biology/mummer/pkg-plist Tue Dec 11 07:23:54 2018 (r487221) +++ head/biology/mummer/pkg-plist Tue Dec 11 07:43:45 2018 (r487222) @@ -3,29 +3,61 @@ bin/combineMUMs bin/delta-filter bin/dnadiff bin/exact-tandems -bin/gaps -bin/mapview -bin/mgaps bin/mummer bin/mummerplot bin/nucmer -bin/nucmer2xfig bin/promer bin/repeat-match -bin/run-mummer1 -bin/run-mummer3 bin/show-aligns bin/show-coords bin/show-diff bin/show-snps bin/show-tiling -libexec/mummer/Foundation.pm +include/mummer-4.0.0beta2/include/compactsufsort/compactsufsort.hpp +include/mummer-4.0.0beta2/include/compactsufsort/compactsufsort_imp.hpp +include/mummer-4.0.0beta2/include/compactsufsort/const_iterator_traits.hpp +include/mummer-4.0.0beta2/include/compactsufsort/divsufsort_private.h +include/mummer-4.0.0beta2/include/compactsufsort/said_traits.hpp +include/mummer-4.0.0beta2/include/compactsufsort/sssort_imp.hpp +include/mummer-4.0.0beta2/include/compactsufsort/trsort_imp.hpp +include/mummer-4.0.0beta2/include/jellyfish/circular_buffer.hpp +include/mummer-4.0.0beta2/include/jellyfish/cooperative_pool2.hpp +include/mummer-4.0.0beta2/include/jellyfish/cpp_array.hpp +include/mummer-4.0.0beta2/include/jellyfish/divisor.hpp +include/mummer-4.0.0beta2/include/jellyfish/stream_manager.hpp +include/mummer-4.0.0beta2/include/jellyfish/whole_sequence_parser.hpp +include/mummer-4.0.0beta2/include/mt_skip_list/common.hpp +include/mummer-4.0.0beta2/include/mt_skip_list/set.hpp +include/mummer-4.0.0beta2/include/mummer/48bit_index.hpp +include/mummer-4.0.0beta2/include/mummer/48bit_iterator.hpp +include/mummer-4.0.0beta2/include/mummer/const_iterator_traits.hpp +include/mummer-4.0.0beta2/include/mummer/delta.hh +include/mummer-4.0.0beta2/include/mummer/dset.hpp +include/mummer-4.0.0beta2/include/mummer/fasta.hpp +include/mummer-4.0.0beta2/include/mummer/mgaps.hh +include/mummer-4.0.0beta2/include/mummer/nucmer.hpp +include/mummer-4.0.0beta2/include/mummer/openmp_qsort.hpp +include/mummer-4.0.0beta2/include/mummer/postnuc.hh +include/mummer-4.0.0beta2/include/mummer/redirect_to_pager.hpp +include/mummer-4.0.0beta2/include/mummer/sparseSA.hpp +include/mummer-4.0.0beta2/include/mummer/sparseSA_imp.hpp +include/mummer-4.0.0beta2/include/mummer/sw_align.hh +include/mummer-4.0.0beta2/include/mummer/sw_alignscore.hh +include/mummer-4.0.0beta2/include/mummer/tigrinc.hh +include/mummer-4.0.0beta2/include/mummer/timer.hpp +include/mummer-4.0.0beta2/include/mummer/translate.hh +include/mummer-4.0.0beta2/include/thread_pipe.hpp +include/mummer-4.0.0beta2/include/thread_pipe/circular_buffer.hpp +include/mummer-4.0.0beta2/include/thread_pipe/cooperative_pool2.hpp +include/mummer-4.0.0beta2/include/thread_pipe/divisor.hpp +include/mummer-4.0.0beta2/include/thread_pipe/traits.hpp +lib/libumdmummer.so +lib/libumdmummer.so.0 +lib/libumdmummer.so.0.0.0 +lib/mummer/Foundation.pm +lib/mummer/tandem-repeat.awk +libdata/pkgconfig/mummer.pc +libexec/mummer/mgaps libexec/mummer/postnuc libexec/mummer/postpro -libexec/mummer/prenuc libexec/mummer/prepro -libexec/mummer/tandem-repeat.awk -%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT -%%PORTDOCS%%%%DOCSDIR%%/INSTALL -%%PORTDOCS%%%%DOCSDIR%%/LICENSE -%%PORTDOCS%%%%DOCSDIR%%/README