Attachment 128639 Details for Bug 172497 – file.diff

[patch] file.diff

file.diff (text/plain), 6.77 KB, created by tkato432 on 2012-10-08 19:10:14 UTC

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Creator: tkato432

Created: 2012-10-08 19:10:14 UTC

Size: 6.77 KB

patch

obsolete

>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 <bsd.port.mk>
>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<score.h>
>+ #include<leftinfluence.h>
>+ #include<rightinfluence.h>
>+-#include<fstream.h>
>++#include<fstream>
>+ 
>+ extern vector<class Score*> 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 <fstream>
>+ #include <iostream>
>+ #include <algorithm>
>++#include <cstring>
>+ 
>+ #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

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Attachments on bug 172497: 128639