From owner-freebsd-ports-bugs@FreeBSD.ORG Mon Oct 8 18:10:17 2012 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [69.147.83.52]) by hub.freebsd.org (Postfix) with ESMTP id 17297106567A for ; Mon, 8 Oct 2012 18:10:17 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 2349B8FC28 for ; Mon, 8 Oct 2012 18:10:14 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.5/8.14.5) with ESMTP id q98IAEHv086309 for ; Mon, 8 Oct 2012 18:10:14 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.5/8.14.5/Submit) id q98IAEW4086308; Mon, 8 Oct 2012 18:10:14 GMT (envelope-from gnats) Resent-Date: Mon, 8 Oct 2012 18:10:14 GMT Resent-Message-Id: <201210081810.q98IAEW4086308@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, KATO Tsuguru Received: from mx1.freebsd.org (mx1.freebsd.org [69.147.83.52]) by hub.freebsd.org (Postfix) with ESMTP id 8E6291065670 for ; Mon, 8 Oct 2012 18:00:31 +0000 (UTC) (envelope-from tkato432@yahoo.com) Received: from msa102lp.auone-net.jp (msa102lp.auone-net.jp [222.3.140.165]) by mx1.freebsd.org (Postfix) with ESMTP id 5085C8FC08 for ; Mon, 8 Oct 2012 18:00:26 +0000 (UTC) Received: from localhost.localdomain (ZT030227.ppp.dion.ne.jp [59.128.30.227]) by msa102lp.auone-net.jp (au one net msa) with ESMTP id 8B4764AC036 for ; Tue, 9 Oct 2012 03:00:15 +0900 (JST) Message-Id: <20121009025553.9acfd1c1d3090f6f1fdba6dd@yahoo.com> Date: Tue, 9 Oct 2012 02:55:53 +0900 From: KATO Tsuguru To: FreeBSD-gnats-submit@FreeBSD.org Cc: Subject: ports/172497: biology/lagan: Update to version 2.0 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 08 Oct 2012 18:10:17 -0000 X-List-Received-Date: Mon, 08 Oct 2012 18:10:17 -0000 >Number: 172497 >Category: ports >Synopsis: biology/lagan: Update to version 2.0 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Oct 08 18:10:14 UTC 2012 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 7.4-RELEASE-p10 i386 >Organization: >Environment: >Description: - Update to version 2.0 New file: files/patch-src__glocal__score.cpp files/patch-src__utils__Glue.cpp Remove file: pkg-plist >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/lagan/Makefile biology/lagan/Makefile --- /usr/ports/biology/lagan/Makefile 2012-10-01 23:45:16.000000000 +0900 +++ biology/lagan/Makefile 2012-10-03 00:25:49.000000000 +0900 @@ -2,7 +2,7 @@ # $FreeBSD: ports/biology/lagan/Makefile,v 1.4 2012/10/01 14:45:16 tabthorpe Exp $ PORTNAME= lagan -PORTVERSION= 1.2 +PORTVERSION= 2.0 CATEGORIES= biology MASTER_SITES= http://lagan.stanford.edu/lagan_web/ DISTNAME= ${PORTNAME}${PORTVERSION:S/.//} @@ -10,10 +10,23 @@ MAINTAINER= ports@FreeBSD.org COMMENT= Efficient tools for large-scale multiple alignments of genomic DNA -LAGAN_DIR= ${PREFIX}/${PORTNAME} +LICENSE= GPLv2 + USE_PERL5_RUN= yes +MAKE_JOBS_UNSAFE=yes + SUB_FILES= pkg-message -SUB_LIST= LAGAN_DIR=${LAGAN_DIR} +SUB_LIST= LAGAN_DIR="${LAGAN_DIR}" + +PLIST_FILES= ${EXECUTABLES:S,^,${PORTNAME}/,} \ + ${SCRIPTS:S,^,${PORTNAME}/,} \ + ${EXEUTILS:S,^,${PORTNAME}/utils/,} \ + ${SCRIPTUTILS:S,^,${PORTNAME}/utils/,} \ + ${READMES:S,^,${PORTNAME}/Readmes/,} +PLIST_DIRS= ${PORTNAME}/utils ${PORTNAME}/Readmes +PLIST_DIRSTRY= ${PORTNAME} + +LAGAN_DIR= ${PREFIX}/${PORTNAME} EXECUTABLES= anchors chaos glocal mlagan order SCRIPTS= anal_gloc.pl lagan.pl rechaos.pl slagan.pl @@ -22,17 +35,19 @@ scorecontigs seqmerge SCRIPTUTILS= cmerge2.pl draft.pl mextract.pl mf2bin.pl mpretty.pl \ mproject.pl mrun.pl mrunfile.pl mrunpairs.pl mviz.pl - -CC:= ${CC} ${CFLAGS} -CPP= ${CXX} ${CXXFLAGS} +READMES= README.FIRST README.chaos README.lagan README.mlagan \ + README.tools README.shuffle post-patch: - @${REINPLACE_CMD} -E 's,^(CC|CPP) =,\1 ?=,g' \ - ${WRKSRC}/Makefile + @${FIND} ${WRKSRC} -name "Makefile" | ${XARGS} ${REINPLACE_CMD} -e \ + '/^CC/s|^|#| ; \ + /^CFLAGS/s|^|#| ; \ + s|$$(CC) -o|$$(CC) $$(CFLAGS) -o| ; \ + s|$$(CPP) -o|$$(CXX) $$(CXXFLAGS) -o| ; \ + s|$$(CLINKER) $$(OPTFLAGS)|$$(CXX) $$(LDFLAGS)|' do-install: @${MKDIR} ${LAGAN_DIR} - ${CP} -R ${WRKSRC}/Readmes ${LAGAN_DIR} .for exe in ${EXECUTABLES} ${INSTALL_PROGRAM} ${WRKSRC}/${exe} ${LAGAN_DIR} .endfor @@ -46,6 +61,10 @@ .for scriptutil in ${SCRIPTUTILS} ${INSTALL_SCRIPT} ${WRKSRC}/utils/${scriptutil} ${LAGAN_DIR}/utils .endfor + @${MKDIR} ${LAGAN_DIR}/Readmes +.for readme in ${READMES} + ${INSTALL_DATA} ${WRKSRC}/Readmes/${readme} ${LAGAN_DIR}/Readmes +.endfor @${CAT} ${PKGMESSAGE} .include diff -urN /usr/ports/biology/lagan/distinfo biology/lagan/distinfo --- /usr/ports/biology/lagan/distinfo 2011-03-19 21:29:32.000000000 +0900 +++ biology/lagan/distinfo 2012-10-02 23:39:12.000000000 +0900 @@ -1,2 +1,2 @@ -SHA256 (lagan12.tar.gz) = d27754367b3aa9bf34976f7a619d5024be444b47cba370e3f53d0bba87389d4a -SIZE (lagan12.tar.gz) = 112894 +SHA256 (lagan20.tar.gz) = a65e61ed4fd6608f4e5ad5b11a1b77f4fec1a207d822c5885b3e86727496e1fe +SIZE (lagan20.tar.gz) = 589115 diff -urN /usr/ports/biology/lagan/files/patch-src__glocal__score.cpp biology/lagan/files/patch-src__glocal__score.cpp --- /usr/ports/biology/lagan/files/patch-src__glocal__score.cpp 1970-01-01 09:00:00.000000000 +0900 +++ biology/lagan/files/patch-src__glocal__score.cpp 2012-10-03 00:24:17.000000000 +0900 @@ -0,0 +1,11 @@ +--- src/glocal/score.cpp.orig 2006-09-15 05:40:19.000000000 +0900 ++++ src/glocal/score.cpp 2012-10-03 00:22:50.000000000 +0900 +@@ -2,7 +2,7 @@ + #include + #include + #include +-#include ++#include + + extern vector scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; + diff -urN /usr/ports/biology/lagan/files/patch-src__utils__Glue.cpp biology/lagan/files/patch-src__utils__Glue.cpp --- /usr/ports/biology/lagan/files/patch-src__utils__Glue.cpp 1970-01-01 09:00:00.000000000 +0900 +++ biology/lagan/files/patch-src__utils__Glue.cpp 2012-10-03 00:24:44.000000000 +0900 @@ -0,0 +1,10 @@ +--- src/utils/Glue.cpp.orig 2006-09-15 05:40:18.000000000 +0900 ++++ src/utils/Glue.cpp 2012-10-03 00:23:38.000000000 +0900 +@@ -6,6 +6,7 @@ + #include + #include + #include ++#include + + #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" + #define MAX_LINE_LENGTH 1024 diff -urN /usr/ports/biology/lagan/pkg-descr biology/lagan/pkg-descr --- /usr/ports/biology/lagan/pkg-descr 2006-03-17 07:31:26.000000000 +0900 +++ biology/lagan/pkg-descr 2012-10-02 23:32:16.000000000 +0900 @@ -1,24 +1,9 @@ -The LAGAN Toolkit consists of four components: +The Lagan Tookit is a set of alignment programs for comparative +genomics. The three main components are a pairwise aligner (LAGAN), a +multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All +three are based on the CHAOS local alignment tool and combine speed +(regions up to several megabases can be aligned in minutes) with high +accuracy. The results of the alignment can be visualized using the VISTA +visualization tool. - CHAOS, a pairwise local aligner optimized for non-coding, and other - poorly conserved regions of the genome. - - LAGAN, a highly parametrizable pairwise global alignment using local - alignments generated by CHAOS as anchors. - - Multi-LAGAN, a progressive pairwise algorithm to produce multiple - sequence alignments. - - Shuffle-LAGAN, a novel glocal algorithm that is able to find - rearrangements in a global alignment. - -Fast and sensitive multiple alignment of long genomic sequences. BMC -Bioinformatics 2003 4:66. - -LAGAN and Multi-LAGAN: efficient tools for large-scale multiple -alignment of genomic DNA. Genome Res 2003 13(4): 721-31. - -Glocal alignment: finding rearrangements during alignment. Proceedings -of the ISMB 2003, Bioinformatics 19: 54i-62i. - -WWW: http://lagan.stanford.edu/lagan_web/ +WWW: http://lagan.stanford.edu/ diff -urN /usr/ports/biology/lagan/pkg-plist biology/lagan/pkg-plist --- /usr/ports/biology/lagan/pkg-plist 2006-03-17 07:31:26.000000000 +0900 +++ biology/lagan/pkg-plist 1970-01-01 09:00:00.000000000 +0900 @@ -1,45 +0,0 @@ -lagan/Readmes/README.mlagan -lagan/Readmes/README.FIRST -lagan/Readmes/README.lagan -lagan/Readmes/README.chaos -lagan/Readmes/README.tools -lagan/Readmes/README.shuffle -lagan/Readmes/LICENSE -lagan/anchors -lagan/chaos -lagan/glocal -lagan/mlagan -lagan/order -lagan/anal_gloc.pl -lagan/lagan.pl -lagan/rechaos.pl -lagan/slagan.pl -lagan/utils/Glue -lagan/utils/bin2bl -lagan/utils/bin2mf -lagan/utils/cextract -lagan/utils/contigorder -lagan/utils/cstat -lagan/utils/dotplot -lagan/utils/fa2xfa -lagan/utils/getbounds -lagan/utils/getcontigpos -lagan/utils/getlength -lagan/utils/getoverlap -lagan/utils/rc -lagan/utils/scorealign -lagan/utils/scorecontigs -lagan/utils/seqmerge -lagan/utils/cmerge2.pl -lagan/utils/draft.pl -lagan/utils/mextract.pl -lagan/utils/mf2bin.pl -lagan/utils/mpretty.pl -lagan/utils/mproject.pl -lagan/utils/mrun.pl -lagan/utils/mrunfile.pl -lagan/utils/mrunpairs.pl -lagan/utils/mviz.pl -@dirrm lagan/Readmes -@dirrmtry lagan/utils -@dirrmtry lagan >Release-Note: >Audit-Trail: >Unformatted: