Date: Wed, 8 Feb 2006 16:22:44 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/93058: [ new port ] biology/lagan Message-ID: <200602081922.k18JMiws043153@omega.iib.unsam.edu.ar> Resent-Message-ID: <200602081930.k18JUCSE010773@freefall.freebsd.org>
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>Number: 93058 >Category: ports >Synopsis: [ new port ] biology/lagan >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: Wed Feb 08 19:30:08 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 6.0-RELEASE-p4 i386 >Organization: IIB-UNSAM >Environment: System: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p4 FreeBSD 6.0-RELEASE-p4 #0: Wed Jan 25 12:43:39 ART 2006 fernan@omega.iib.unsam.edu.ar:/usr/obj/usr/src/sys/OMEGA i386 >Description: >How-To-Repeat: >Fix: --- lagan.shar begins here --- # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # lagan # lagan/Makefile # lagan/pkg-descr # lagan/distinfo # lagan/pkg-plist # lagan/files # lagan/files/pkg-message.in # echo c - lagan mkdir -p lagan > /dev/null 2>&1 echo x - lagan/Makefile sed 's/^X//' >lagan/Makefile << 'END-of-lagan/Makefile' X# ex:ts=8 X# New ports collection makefile for: lagan X# Date created: 07 Dec 2005 X# Whom: Fernan Aguero <fernan@iib.unsam.edu.ar> X# X# $FreeBSD$ X# X XPORTNAME= lagan XPORTVERSION= 1.2 XCATEGORIES= biology XMASTER_SITES= http://lagan.stanford.edu/lagan_web/ XDISTNAME= ${PORTNAME}${PORTVERSION:S/.//} X XMAINTAINER= fernan@iib.unsam.edu.ar XCOMMENT= Efficient tools for large-scale multiple alignments of genomic DNA X XLAGAN_DIR= ${PREFIX}/${PORTNAME} XUSE_PERL5_RUN= yes XSUB_FILES= pkg-message XSUB_LIST= LAGAN_DIR=${LAGAN_DIR} X XEXECUTABLES= anchors chaos glocal mlagan order XSCRIPTS= anal_gloc.pl lagan.pl rechaos.pl slagan.pl XEXEUTILS= Glue bin2bl bin2mf cextract contigorder cstat dotplot fa2xfa \ X getbounds getcontigpos getlength getoverlap rc scorealign \ X scorecontigs seqmerge XSCRIPTUTILS= cmerge2.pl draft.pl mextract.pl mf2bin.pl mpretty.pl \ X mproject.pl mrun.pl mrunfile.pl mrunpairs.pl mviz.pl X Xdo-install: X @${MKDIR} ${LAGAN_DIR} X ${CP} -R ${WRKSRC}/Readmes ${LAGAN_DIR} X.for exe in ${EXECUTABLES} X ${INSTALL_PROGRAM} ${WRKSRC}/${exe} ${LAGAN_DIR} X.endfor X.for script in ${SCRIPTS} X ${INSTALL_SCRIPT} ${WRKSRC}/${script} ${LAGAN_DIR} X.endfor X @${MKDIR} ${LAGAN_DIR}/utils X.for exeutil in ${EXEUTILS} X ${INSTALL_PROGRAM} ${WRKSRC}/utils/${exeutil} ${LAGAN_DIR}/utils X.endfor X.for scriptutil in ${SCRIPTUTILS} X ${INSTALL_SCRIPT} ${WRKSRC}/utils/${scriptutil} ${LAGAN_DIR}/utils X.endfor X @${CAT} ${PKGMESSAGE} X X.include <bsd.port.mk> END-of-lagan/Makefile echo x - lagan/pkg-descr sed 's/^X//' >lagan/pkg-descr << 'END-of-lagan/pkg-descr' XThe LAGAN Toolkit consists of four components: X X CHAOS, a pairwise local aligner optimized for non-coding, and other X poorly conserved regions of the genome. X X LAGAN, a highly parametrizable pairwise global alignment using local X alignments generated by CHAOS as anchors. X X Multi-LAGAN, a progressive pairwise algorithm to produce multiple X sequence alignments. X X Shuffle-LAGAN, a novel glocal algorithm that is able to find X rearrangements in a global alignment. X XFast and sensitive multiple alignment of long genomic sequences. BMC XBioinformatics 2003 4:66. X XLAGAN and Multi-LAGAN: efficient tools for large-scale multiple Xalignment of genomic DNA. Genome Res 2003 13(4): 721-31. X XGlocal alignment: finding rearrangements during alignment. Proceedings Xof the ISMB 2003, Bioinformatics 19: 54i-62i. X XWWW: http://lagan.stanford.edu/lagan_web/ END-of-lagan/pkg-descr echo x - lagan/distinfo sed 's/^X//' >lagan/distinfo << 'END-of-lagan/distinfo' XMD5 (lagan12.tar.gz) = e45c9287d04b31924115869588f1fb61 XSHA256 (lagan12.tar.gz) = d27754367b3aa9bf34976f7a619d5024be444b47cba370e3f53d0bba87389d4a XSIZE (lagan12.tar.gz) = 112894 END-of-lagan/distinfo echo x - lagan/pkg-plist sed 's/^X//' >lagan/pkg-plist << 'END-of-lagan/pkg-plist' Xlagan/Readmes/README.mlagan Xlagan/Readmes/README.FIRST Xlagan/Readmes/README.lagan Xlagan/Readmes/README.chaos Xlagan/Readmes/README.tools Xlagan/Readmes/README.shuffle Xlagan/Readmes/LICENSE Xlagan/anchors Xlagan/chaos Xlagan/glocal Xlagan/mlagan Xlagan/order Xlagan/anal_gloc.pl Xlagan/lagan.pl Xlagan/rechaos.pl Xlagan/slagan.pl Xlagan/utils/Glue Xlagan/utils/bin2bl Xlagan/utils/bin2mf Xlagan/utils/cextract Xlagan/utils/contigorder Xlagan/utils/cstat Xlagan/utils/dotplot Xlagan/utils/fa2xfa Xlagan/utils/getbounds Xlagan/utils/getcontigpos Xlagan/utils/getlength Xlagan/utils/getoverlap Xlagan/utils/rc Xlagan/utils/scorealign Xlagan/utils/scorecontigs Xlagan/utils/seqmerge Xlagan/utils/cmerge2.pl Xlagan/utils/draft.pl Xlagan/utils/mextract.pl Xlagan/utils/mf2bin.pl Xlagan/utils/mpretty.pl Xlagan/utils/mproject.pl Xlagan/utils/mrun.pl Xlagan/utils/mrunfile.pl Xlagan/utils/mrunpairs.pl Xlagan/utils/mviz.pl X@dirrm lagan/Readmes X@unexec rmdir %Dlagan/utils 2>/dev/null || true X@unexec rmdir %Dlagan 2>/dev/null || true END-of-lagan/pkg-plist echo c - lagan/files mkdir -p lagan/files > /dev/null 2>&1 echo x - lagan/files/pkg-message.in sed 's/^X//' >lagan/files/pkg-message.in << 'END-of-lagan/files/pkg-message.in' X=============================================================================== X X All the executables, scripts, Readmes and utilities were installed X under %%LAGAN_DIR%% X X Add this to your PATH and set the environment variable X LAGAN_DIR to point to this directory. X X=============================================================================== END-of-lagan/files/pkg-message.in exit --- lagan.shar ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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