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- Update to version 2.0
- Update pkg-descr PR: 172497 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Feature safe: yes
This commit is contained in:
parent
8a810e1148
commit
2a3cdaf773
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=307436
@ -2,7 +2,7 @@
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# $FreeBSD$
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PORTNAME= lagan
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PORTVERSION= 1.2
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PORTVERSION= 2.0
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CATEGORIES= biology
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MASTER_SITES= http://lagan.stanford.edu/lagan_web/
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DISTNAME= ${PORTNAME}${PORTVERSION:S/.//}
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@ -10,10 +10,23 @@ DISTNAME= ${PORTNAME}${PORTVERSION:S/.//}
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MAINTAINER= ports@FreeBSD.org
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COMMENT= Efficient tools for large-scale multiple alignments of genomic DNA
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LAGAN_DIR= ${PREFIX}/${PORTNAME}
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LICENSE= GPLv2
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USE_PERL5_RUN= yes
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MAKE_JOBS_UNSAFE=yes
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SUB_FILES= pkg-message
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SUB_LIST= LAGAN_DIR=${LAGAN_DIR}
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SUB_LIST= LAGAN_DIR="${LAGAN_DIR}"
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PLIST_FILES= ${EXECUTABLES:S,^,${PORTNAME}/,} \
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${SCRIPTS:S,^,${PORTNAME}/,} \
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${EXEUTILS:S,^,${PORTNAME}/utils/,} \
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${SCRIPTUTILS:S,^,${PORTNAME}/utils/,} \
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${READMES:S,^,${PORTNAME}/Readmes/,}
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PLIST_DIRS= ${PORTNAME}/utils ${PORTNAME}/Readmes
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PLIST_DIRSTRY= ${PORTNAME}
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LAGAN_DIR= ${PREFIX}/${PORTNAME}
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EXECUTABLES= anchors chaos glocal mlagan order
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SCRIPTS= anal_gloc.pl lagan.pl rechaos.pl slagan.pl
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@ -22,17 +35,19 @@ EXEUTILS= Glue bin2bl bin2mf cextract contigorder cstat dotplot fa2xfa \
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scorecontigs seqmerge
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SCRIPTUTILS= cmerge2.pl draft.pl mextract.pl mf2bin.pl mpretty.pl \
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mproject.pl mrun.pl mrunfile.pl mrunpairs.pl mviz.pl
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CC:= ${CC} ${CFLAGS}
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CPP= ${CXX} ${CXXFLAGS}
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READMES= README.FIRST README.chaos README.lagan README.mlagan \
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README.tools README.shuffle
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post-patch:
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@${REINPLACE_CMD} -E 's,^(CC|CPP) =,\1 ?=,g' \
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${WRKSRC}/Makefile
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@${FIND} ${WRKSRC} -name "Makefile" | ${XARGS} ${REINPLACE_CMD} -e \
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'/^CC/s|^|#| ; \
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/^CFLAGS/s|^|#| ; \
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s|$$(CC) -o|$$(CC) $$(CFLAGS) -o| ; \
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s|$$(CPP) -o|$$(CXX) $$(CXXFLAGS) -o| ; \
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s|$$(CLINKER) $$(OPTFLAGS)|$$(CXX) $$(LDFLAGS)|'
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do-install:
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@${MKDIR} ${LAGAN_DIR}
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${CP} -R ${WRKSRC}/Readmes ${LAGAN_DIR}
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.for exe in ${EXECUTABLES}
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${INSTALL_PROGRAM} ${WRKSRC}/${exe} ${LAGAN_DIR}
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.endfor
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@ -45,6 +60,10 @@ do-install:
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.endfor
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.for scriptutil in ${SCRIPTUTILS}
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${INSTALL_SCRIPT} ${WRKSRC}/utils/${scriptutil} ${LAGAN_DIR}/utils
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.endfor
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@${MKDIR} ${LAGAN_DIR}/Readmes
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.for readme in ${READMES}
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${INSTALL_DATA} ${WRKSRC}/Readmes/${readme} ${LAGAN_DIR}/Readmes
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.endfor
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@${CAT} ${PKGMESSAGE}
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@ -1,2 +1,2 @@
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SHA256 (lagan12.tar.gz) = d27754367b3aa9bf34976f7a619d5024be444b47cba370e3f53d0bba87389d4a
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SIZE (lagan12.tar.gz) = 112894
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SHA256 (lagan20.tar.gz) = a65e61ed4fd6608f4e5ad5b11a1b77f4fec1a207d822c5885b3e86727496e1fe
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SIZE (lagan20.tar.gz) = 589115
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11
biology/lagan/files/patch-src__glocal__score.cpp
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11
biology/lagan/files/patch-src__glocal__score.cpp
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@ -0,0 +1,11 @@
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--- src/glocal/score.cpp.orig 2006-09-15 05:40:19.000000000 +0900
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+++ src/glocal/score.cpp 2012-10-03 00:22:50.000000000 +0900
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@@ -2,7 +2,7 @@
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#include<score.h>
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#include<leftinfluence.h>
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#include<rightinfluence.h>
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-#include<fstream.h>
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+#include<fstream>
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extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
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biology/lagan/files/patch-src__utils__Glue.cpp
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10
biology/lagan/files/patch-src__utils__Glue.cpp
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@ -0,0 +1,10 @@
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--- src/utils/Glue.cpp.orig 2006-09-15 05:40:18.000000000 +0900
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+++ src/utils/Glue.cpp 2012-10-03 00:23:38.000000000 +0900
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@@ -6,6 +6,7 @@
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#include <fstream>
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#include <iostream>
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#include <algorithm>
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+#include <cstring>
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#define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
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#define MAX_LINE_LENGTH 1024
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@ -1,24 +1,9 @@
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The LAGAN Toolkit consists of four components:
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The Lagan Tookit is a set of alignment programs for comparative
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genomics. The three main components are a pairwise aligner (LAGAN), a
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multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All
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three are based on the CHAOS local alignment tool and combine speed
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(regions up to several megabases can be aligned in minutes) with high
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accuracy. The results of the alignment can be visualized using the VISTA
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visualization tool.
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CHAOS, a pairwise local aligner optimized for non-coding, and other
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poorly conserved regions of the genome.
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LAGAN, a highly parametrizable pairwise global alignment using local
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alignments generated by CHAOS as anchors.
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Multi-LAGAN, a progressive pairwise algorithm to produce multiple
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sequence alignments.
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Shuffle-LAGAN, a novel glocal algorithm that is able to find
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rearrangements in a global alignment.
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Fast and sensitive multiple alignment of long genomic sequences. BMC
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Bioinformatics 2003 4:66.
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LAGAN and Multi-LAGAN: efficient tools for large-scale multiple
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alignment of genomic DNA. Genome Res 2003 13(4): 721-31.
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Glocal alignment: finding rearrangements during alignment. Proceedings
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of the ISMB 2003, Bioinformatics 19: 54i-62i.
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WWW: http://lagan.stanford.edu/lagan_web/
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WWW: http://lagan.stanford.edu/
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@ -1,45 +0,0 @@
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lagan/Readmes/README.mlagan
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lagan/Readmes/README.FIRST
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lagan/Readmes/README.lagan
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lagan/Readmes/README.chaos
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lagan/Readmes/README.tools
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lagan/Readmes/README.shuffle
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lagan/Readmes/LICENSE
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lagan/anchors
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lagan/chaos
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lagan/glocal
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lagan/mlagan
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lagan/order
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lagan/anal_gloc.pl
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lagan/lagan.pl
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lagan/rechaos.pl
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lagan/slagan.pl
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lagan/utils/Glue
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lagan/utils/bin2bl
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lagan/utils/bin2mf
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lagan/utils/cextract
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lagan/utils/contigorder
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lagan/utils/cstat
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lagan/utils/dotplot
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lagan/utils/fa2xfa
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lagan/utils/getbounds
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lagan/utils/getcontigpos
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lagan/utils/getlength
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lagan/utils/getoverlap
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lagan/utils/rc
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lagan/utils/scorealign
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lagan/utils/scorecontigs
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lagan/utils/seqmerge
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lagan/utils/cmerge2.pl
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lagan/utils/draft.pl
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lagan/utils/mextract.pl
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lagan/utils/mf2bin.pl
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lagan/utils/mpretty.pl
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lagan/utils/mproject.pl
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lagan/utils/mrun.pl
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lagan/utils/mrunfile.pl
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lagan/utils/mrunpairs.pl
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lagan/utils/mviz.pl
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@dirrm lagan/Readmes
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@dirrmtry lagan/utils
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@dirrmtry lagan
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