Date: Thu, 15 Nov 2012 07:04:29 +0000 (UTC) From: Wen Heping <wen@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r307436 - in head/biology/lagan: . files Message-ID: <201211150704.qAF74Tcp040503@svn.freebsd.org>
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Author: wen Date: Thu Nov 15 07:04:29 2012 New Revision: 307436 URL: http://svnweb.freebsd.org/changeset/ports/307436 Log: - Update to version 2.0 - Update pkg-descr PR: 172497 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Feature safe: yes Added: head/biology/lagan/files/patch-src__glocal__score.cpp (contents, props changed) head/biology/lagan/files/patch-src__utils__Glue.cpp (contents, props changed) Deleted: head/biology/lagan/pkg-plist Modified: head/biology/lagan/Makefile head/biology/lagan/distinfo head/biology/lagan/pkg-descr Modified: head/biology/lagan/Makefile ============================================================================== --- head/biology/lagan/Makefile Thu Nov 15 06:56:25 2012 (r307435) +++ head/biology/lagan/Makefile Thu Nov 15 07:04:29 2012 (r307436) @@ -2,7 +2,7 @@ # $FreeBSD$ 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 @@ DISTNAME= ${PORTNAME}${PORTVERSION:S/.// 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 @@ EXEUTILS= Glue bin2bl bin2mf cextract co 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 @@ do-install: .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 <bsd.port.mk> Modified: head/biology/lagan/distinfo ============================================================================== --- head/biology/lagan/distinfo Thu Nov 15 06:56:25 2012 (r307435) +++ head/biology/lagan/distinfo Thu Nov 15 07:04:29 2012 (r307436) @@ -1,2 +1,2 @@ -SHA256 (lagan12.tar.gz) = d27754367b3aa9bf34976f7a619d5024be444b47cba370e3f53d0bba87389d4a -SIZE (lagan12.tar.gz) = 112894 +SHA256 (lagan20.tar.gz) = a65e61ed4fd6608f4e5ad5b11a1b77f4fec1a207d822c5885b3e86727496e1fe +SIZE (lagan20.tar.gz) = 589115 Added: head/biology/lagan/files/patch-src__glocal__score.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/lagan/files/patch-src__glocal__score.cpp Thu Nov 15 07:04:29 2012 (r307436) @@ -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<score.h> + #include<leftinfluence.h> + #include<rightinfluence.h> +-#include<fstream.h> ++#include<fstream> + + extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; + Added: head/biology/lagan/files/patch-src__utils__Glue.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/lagan/files/patch-src__utils__Glue.cpp Thu Nov 15 07:04:29 2012 (r307436) @@ -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 <fstream> + #include <iostream> + #include <algorithm> ++#include <cstring> + + #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" + #define MAX_LINE_LENGTH 1024 Modified: head/biology/lagan/pkg-descr ============================================================================== --- head/biology/lagan/pkg-descr Thu Nov 15 06:56:25 2012 (r307435) +++ head/biology/lagan/pkg-descr Thu Nov 15 07:04:29 2012 (r307436) @@ -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/
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