Attachment #128639 for bug #172497

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Lines 2-8 Link Here

(-)biology/lagan/Makefile (-9 / +28 lines)
2	# $FreeBSD: ports/biology/lagan/Makefile,v 1.4 2012/10/01 14:45:16 tabthorpe Exp $	2	# $FreeBSD: ports/biology/lagan/Makefile,v 1.4 2012/10/01 14:45:16 tabthorpe Exp $
3		3
4	PORTNAME= lagan	4	PORTNAME= lagan
5	PORTVERSION= 1.2	5	PORTVERSION= 2.0
6	CATEGORIES= biology	6	CATEGORIES= biology
7	MASTER_SITES= http://lagan.stanford.edu/lagan_web/	7	MASTER_SITES= http://lagan.stanford.edu/lagan_web/
8	DISTNAME= ${PORTNAME}${PORTVERSION:S/.//}	8	DISTNAME= ${PORTNAME}${PORTVERSION:S/.//}
Lines 10-19 Link Here
10	MAINTAINER= ports@FreeBSD.org	10	MAINTAINER= ports@FreeBSD.org
11	COMMENT= Efficient tools for large-scale multiple alignments of genomic DNA	11	COMMENT= Efficient tools for large-scale multiple alignments of genomic DNA
12		12
13	LAGAN_DIR= ${PREFIX}/${PORTNAME}	13	LICENSE= GPLv2
		14
14	USE_PERL5_RUN= yes	15	USE_PERL5_RUN= yes
		16	MAKE_JOBS_UNSAFE=yes
		17
15	SUB_FILES= pkg-message	18	SUB_FILES= pkg-message
16	SUB_LIST= LAGAN_DIR=${LAGAN_DIR}	19	SUB_LIST= LAGAN_DIR="${LAGAN_DIR}"
		20
		21	PLIST_FILES= ${EXECUTABLES:S,^,${PORTNAME}/,} \
		22	${SCRIPTS:S,^,${PORTNAME}/,} \
		23	${EXEUTILS:S,^,${PORTNAME}/utils/,} \
		24	${SCRIPTUTILS:S,^,${PORTNAME}/utils/,} \
		25	${READMES:S,^,${PORTNAME}/Readmes/,}
		26	PLIST_DIRS= ${PORTNAME}/utils ${PORTNAME}/Readmes
		27	PLIST_DIRSTRY= ${PORTNAME}
		28
		29	LAGAN_DIR= ${PREFIX}/${PORTNAME}
17		30
18	EXECUTABLES= anchors chaos glocal mlagan order	31	EXECUTABLES= anchors chaos glocal mlagan order
19	SCRIPTS= anal_gloc.pl lagan.pl rechaos.pl slagan.pl	32	SCRIPTS= anal_gloc.pl lagan.pl rechaos.pl slagan.pl
Lines 22-38 Link Here
22	scorecontigs seqmerge	35	scorecontigs seqmerge
23	SCRIPTUTILS= cmerge2.pl draft.pl mextract.pl mf2bin.pl mpretty.pl \	36	SCRIPTUTILS= cmerge2.pl draft.pl mextract.pl mf2bin.pl mpretty.pl \
24	mproject.pl mrun.pl mrunfile.pl mrunpairs.pl mviz.pl	37	mproject.pl mrun.pl mrunfile.pl mrunpairs.pl mviz.pl
25		38	READMES= README.FIRST README.chaos README.lagan README.mlagan \
26	CC:= ${CC} ${CFLAGS}	39	README.tools README.shuffle
27	CPP= ${CXX} ${CXXFLAGS}
28		40
29	post-patch:	41	post-patch:
30	@${REINPLACE_CMD} -E 's,^(CC\|CPP) =,\1 ?=,g' \	42	@${FIND} ${WRKSRC} -name "Makefile" \| ${XARGS} ${REINPLACE_CMD} -e \
31	${WRKSRC}/Makefile	43	'/^CC/s\|^\|#\| ; \
		44	/^CFLAGS/s\|^\|#\| ; \
		45	s\|$$(CC) -o\|$$(CC) $$(CFLAGS) -o\| ; \
		46	s\|$$(CPP) -o\|$$(CXX) $$(CXXFLAGS) -o\| ; \
		47	s\|$$(CLINKER) $$(OPTFLAGS)\|$$(CXX) $$(LDFLAGS)\|'
32		48
33	do-install:	49	do-install:
34	@${MKDIR} ${LAGAN_DIR}	50	@${MKDIR} ${LAGAN_DIR}
35	${CP} -R ${WRKSRC}/Readmes ${LAGAN_DIR}
36	.for exe in ${EXECUTABLES}	51	.for exe in ${EXECUTABLES}
37	${INSTALL_PROGRAM} ${WRKSRC}/${exe} ${LAGAN_DIR}	52	${INSTALL_PROGRAM} ${WRKSRC}/${exe} ${LAGAN_DIR}
38	.endfor	53	.endfor
Lines 46-51 Link Here
46	.for scriptutil in ${SCRIPTUTILS}	61	.for scriptutil in ${SCRIPTUTILS}
47	${INSTALL_SCRIPT} ${WRKSRC}/utils/${scriptutil} ${LAGAN_DIR}/utils	62	${INSTALL_SCRIPT} ${WRKSRC}/utils/${scriptutil} ${LAGAN_DIR}/utils
48	.endfor	63	.endfor
		64	@${MKDIR} ${LAGAN_DIR}/Readmes
		65	.for readme in ${READMES}
		66	${INSTALL_DATA} ${WRKSRC}/Readmes/${readme} ${LAGAN_DIR}/Readmes
		67	.endfor
49	@${CAT} ${PKGMESSAGE}	68	@${CAT} ${PKGMESSAGE}
50		69
51	.include <bsd.port.mk>	70	.include <bsd.port.mk>

Lines 1-2 Link Here

(-)biology/lagan/distinfo (-2 / +2 lines)
1	SHA256 (lagan12.tar.gz) = d27754367b3aa9bf34976f7a619d5024be444b47cba370e3f53d0bba87389d4a	1	SHA256 (lagan20.tar.gz) = a65e61ed4fd6608f4e5ad5b11a1b77f4fec1a207d822c5885b3e86727496e1fe
2	SIZE (lagan12.tar.gz) = 112894	2	SIZE (lagan20.tar.gz) = 589115

Line 0 Link Here

(-)biology/lagan/files/patch-src__glocal__score.cpp (+11 lines)
	1	--- src/glocal/score.cpp.orig 2006-09-15 05:40:19.000000000 +0900
	2	+++ src/glocal/score.cpp 2012-10-03 00:22:50.000000000 +0900
	3	@@ -2,7 +2,7 @@
	4	#include<score.h>
	5	#include<leftinfluence.h>
	6	#include<rightinfluence.h>
	7	-#include<fstream.h>
	8	+#include<fstream>
	9
	10	extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
	11

Line 0 Link Here

(-)biology/lagan/files/patch-src__utils__Glue.cpp (+10 lines)
	1	--- src/utils/Glue.cpp.orig 2006-09-15 05:40:18.000000000 +0900
	2	+++ src/utils/Glue.cpp 2012-10-03 00:23:38.000000000 +0900
	3	@@ -6,6 +6,7 @@
	4	#include <fstream>
	5	#include <iostream>
	6	#include <algorithm>
	7	+#include <cstring>
	8
	9	#define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
	10	#define MAX_LINE_LENGTH 1024




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.

WWW: http://lagan.stanford.edu/
 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/




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

Return to bug 172497

Lines 1-24 Link Here

(-)biology/lagan/pkg-descr (-23 / +8 lines)
1	The LAGAN Toolkit consists of four components:	1	The Lagan Tookit is a set of alignment programs for comparative
		2	genomics. The three main components are a pairwise aligner (LAGAN), a
		3	multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All
		4	three are based on the CHAOS local alignment tool and combine speed
		5	(regions up to several megabases can be aligned in minutes) with high
		6	accuracy. The results of the alignment can be visualized using the VISTA
		7	visualization tool.
2		8
3	CHAOS, a pairwise local aligner optimized for non-coding, and other	9	WWW: http://lagan.stanford.edu/
4	poorly conserved regions of the genome.
5
6	LAGAN, a highly parametrizable pairwise global alignment using local
7	alignments generated by CHAOS as anchors.
8
9	Multi-LAGAN, a progressive pairwise algorithm to produce multiple
10	sequence alignments.
11
12	Shuffle-LAGAN, a novel glocal algorithm that is able to find
13	rearrangements in a global alignment.
14
15	Fast and sensitive multiple alignment of long genomic sequences. BMC
16	Bioinformatics 2003 4:66.
17
18	LAGAN and Multi-LAGAN: efficient tools for large-scale multiple
19	alignment of genomic DNA. Genome Res 2003 13(4): 721-31.
20
21	Glocal alignment: finding rearrangements during alignment. Proceedings
22	of the ISMB 2003, Bioinformatics 19: 54i-62i.
23
24	WWW: http://lagan.stanford.edu/lagan_web/

Lines 1-45 Link Here

(-)biology/lagan/pkg-plist (-45 lines)
1	lagan/Readmes/README.mlagan
2	lagan/Readmes/README.FIRST
3	lagan/Readmes/README.lagan
4	lagan/Readmes/README.chaos
5	lagan/Readmes/README.tools
6	lagan/Readmes/README.shuffle
7	lagan/Readmes/LICENSE
8	lagan/anchors
9	lagan/chaos
10	lagan/glocal
11	lagan/mlagan
12	lagan/order
13	lagan/anal_gloc.pl
14	lagan/lagan.pl
15	lagan/rechaos.pl
16	lagan/slagan.pl
17	lagan/utils/Glue
18	lagan/utils/bin2bl
19	lagan/utils/bin2mf
20	lagan/utils/cextract
21	lagan/utils/contigorder
22	lagan/utils/cstat
23	lagan/utils/dotplot
24	lagan/utils/fa2xfa
25	lagan/utils/getbounds
26	lagan/utils/getcontigpos
27	lagan/utils/getlength
28	lagan/utils/getoverlap
29	lagan/utils/rc
30	lagan/utils/scorealign
31	lagan/utils/scorecontigs
32	lagan/utils/seqmerge
33	lagan/utils/cmerge2.pl
34	lagan/utils/draft.pl
35	lagan/utils/mextract.pl
36	lagan/utils/mf2bin.pl
37	lagan/utils/mpretty.pl
38	lagan/utils/mproject.pl
39	lagan/utils/mrun.pl
40	lagan/utils/mrunfile.pl
41	lagan/utils/mrunpairs.pl
42	lagan/utils/mviz.pl
43	@dirrm lagan/Readmes
44	@dirrmtry lagan/utils
45	@dirrmtry lagan